 Case 11 (XFP): Denmark/DCGC-692222/2025



Target: 9 samples            Number of changes: 146                                                                          
BC: LF.7.9 + A.2.5.1 + LF.7.9 BC BR: 134-135, 136-137                   BC BR coord: 27810 - 27811, 28145 - 28146      
Direction L1: >>             Initial region span: 1-134,135-136,141-146 Gap history (edge excluded): 134-141 -> 136-141
Alt. candidates: [], []                                                                                                             
Model 1BP/2BP comparison:    2BP vs 1BP: 5.93e-02                                                                                   
Rec. model vs L1: 2.89e-16   Rec. model vs L2: 0.00e+00                                                                      
Flags: Model_2BP_Best

LF.7.9 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7.9	20	134	204.080142	NaN	NaN	NaN	*	*	*
XFJ.3	14	116	203.689067	190.056827	-42.113654	5.829466e-05	*
XFJ.1	59	116	203.361657	194.696687	-51.393374	6.036083e-03	*
JN.1.4	8971	134	166.141072	176.399125	-14.798251	6.844436e-11		*
LF.7	58	134	153.506696	149.378940	39.242120	1.260958e-22		*
JN.1	17255	134	143.567535	152.644170	32.711659	3.301203e-21		*
LF.7.2.1	67	134	140.394377	147.541603	42.916795	2.002622e-23		*
LF.7.1	165	135	137.220118	144.581697	48.836606	1.037737e-24		*
LF.7.9.1	48	134	136.458760	132.349838	73.300323	5.066006e-30		*
LF.7.1.2	26	134	133.802412	129.762335	78.475331	3.800520e-31		*

|||||

A.2.5.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
A.2.5.1	25	136	8.760478	NaN	NaN	NaN	*	*	*
A.2.5	513	136	6.835739	6.835739	-9.671479	0.145876	*	*
B.1.1.149	55	135	5.220104	-4.779896	13.559792	0.000001		*
CH.1.1.9	97	135	5.220104	-4.779896	13.559792	0.000001		*
CH.1.1.13	145	135	5.213183	-4.786817	13.573633	0.000001		*
CH.1.1.14	88	135	5.197114	-4.802886	13.605771	0.000001		*
AY.62	1056	135	5.193231	-4.806769	13.613538	0.000001		*
BR.2.1	313	135	5.190928	-4.809072	13.618143	0.000001		*
NL.18	10	135	5.114743	-4.885257	13.770513	0.000001		*
MC.2	396	140	5.113976	2.501432	-1.002865	0.001911	*

|||||

LF.7.9 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7.9	20	141	7.496435	None	None	None	*	*	*

Target sequence

, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3784_C|T, 4184_G|A, 4321_C|T, 4369_T|C, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10954_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C,
17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20384_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25494_G|A, 25584_C|T, 25599_G|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28093_C|T, 28144_T|C, 28271_A|T,
28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 11 (XFP): OZ285414



Target: 9 samples         Number of changes: 151                                                       
BC: XFJ.1 + MC.2          BC BR: 119-120                    BC BR coord: 25216 - 25217          
Direction L1: >>          Initial region span: 1-119,123-151 Gap history (edge excluded): 119-123
Alt. candidates: [], []                                                                                       
Model 1BP/2BP comparison: 1BP vs 2BP: 1.89e-02                                                                
Rec. model vs L1: 1.18e-60 Rec. model vs L2: 3.06e-139                                                  
Flags: Model_1BP_Best

XFJ.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	119	181.384545	NaN	NaN	NaN	*	*	*
LF.7.9	20	137	177.626648	168.600273	-41.200547	2.802496e-06
XFJ.3	14	119	168.317700	168.317700	-40.635400	2.118081e-06		*
JN.1	17255	137	148.474683	120.641301	54.717397	4.157016e-27
JN.1.4	8971	137	146.200272	118.757915	58.484170	6.343195e-28
PY.1	82	119	134.256585	134.256585	27.486830	3.401740e-21		*
LF.7	58	137	128.987966	119.573868	56.852265	1.433039e-27
LF.7.9.3	20	107	128.180951	124.377896	47.244208	1.750020e-25
KP.2.3	4440	137	120.509237	107.334479	81.331041	6.926177e-33
JN.1.16.1	466	138	120.276038	110.810640	74.378720	2.237005e-31

|||||

MC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.2	396	123	44.449423	NaN	NaN	NaN	*	*	*
KP.3.1.1	12013	121	35.668647	35.395693	-2.791385	2.650265e+04	*
JN.1.20	66	123	35.429427	16.191774	35.616452	1.209661e-04	*	*
KP.3.1	1957	123	32.321589	13.083937	41.832127	5.422248e-06		*
MC.10	221	123	31.699491	12.461839	43.076322	2.902320e-06		*
KP.3	769	120	31.389966	31.389966	5.220068	4.829920e+02	*
MC.19	221	123	31.343269	12.105617	43.788767	2.035030e-06		*
NY.15	216	123	30.529708	-2.347172	72.694345	1.078985e-12		*
MC.16	917	123	29.278353	10.040700	47.918600	2.580790e-07		*
JN.1.46	308	121	28.922346	18.922346	30.155309	1.854760e-03	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3784_C|T, 4184_G|A, 4321_C|T, 4369_T|C, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 10954_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14371_G|A, 14408_C|T, 15714_C|T, 15756_T|A, 15783_C|T,
16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20384_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T,
25494_G|A, 25584_C|T, 25599_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28093_C|T, 28144_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T, 28877_A|T, 28878_G|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 11 (XFP): USA/CA-GBW-GKISBBBE89075/2025



Target: 9 samples          Number of changes: 149                                                 
BC: KP.2.28.1 + XFJ.1      BC BR: 12-13                   BC BR coord: 5240 - 5241         
Direction L1: <<           Initial region span: 1-8,13-149 Gap history (edge excluded): 8-13
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  1BP vs 2BP: 4.71e-02                                                          
Rec. model vs L1: 1.61e-129 Rec. model vs L2: 2.57e-25                                             
Flags: Model_1BP_Best

KP.2.28.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.28.1	10	8	18.811150	NaN	NaN	NaN	*	*	*
LP.1	659	11	17.020940	1.332105	27.335791	1.447735	*
LF.1.1.1	109	8	16.348047	-10.543103	51.086206	0.000010	*	*
BA.2.86.1	1343	11	16.191494	6.191494	17.617013	186.792804	*
KP.3.1.1	12013	11	15.885304	5.885304	18.229391	137.689342	*
JN.1.31	204	8	15.720993	-2.132149	34.264297	0.045502	*	*
KP.3.1	1957	8	15.233281	-2.623443	35.246886	0.027737	*	*
KP.2.3	4440	11	13.894198	3.894198	22.211604	18.821503	*
JN.1.39	1007	11	10.874362	0.874362	28.251276	0.918512	*
MG.1	23	11	8.835060	-1.164940	32.329880	0.119433	*

|||||

XFJ.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	13	195.146903	NaN	NaN	NaN	*	*	*
LF.7.9	20	25	176.417928	172.803235	-21.606470	1.985461e-10
XFJ.3	14	13	172.658536	172.658536	-21.317072	1.717468e-10		*
JN.1.4	8971	5	164.445377	152.584793	18.830415	3.284179e-19
LF.7.1	165	25	155.105209	145.815757	32.368487	3.769235e-22
PY.2	17	25	149.216202	136.978220	50.043560	5.486071e-26
LF.7	58	25	144.019777	140.387692	43.224616	1.660373e-24
LF.7.2.1	67	25	143.102115	139.487422	45.025155	6.716904e-25
LF.7.6.2	17	25	136.675995	133.061302	57.877395	1.088497e-27
PY.1	82	25	136.662298	124.114296	75.771407	1.419263e-31

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2172_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3784_C|T, 4184_G|A, 4321_C|T, 4369_T|C, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10954_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 13427_G|A, 14408_C|T, 15714_C|T, 15756_T|A,
16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20384_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23230_C|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T,
25494_G|A, 25584_C|T, 25599_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28093_C|T, 28144_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 11 (XFP): USA/MA-MASPHL-14151/2025



Target: 9 samples          Number of changes: 154                                                   
BC: MC.11 + XFJ.1          BC BR: 17-18                    BC BR coord: 5240 - 5241          
Direction L1: <<           Initial region span: 1-11,18-154 Gap history (edge excluded): 11-18
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  1BP vs 2BP: 2.45e-02                                                            
Rec. model vs L1: 3.93e-154 Rec. model vs L2: 2.20e-30                                               
Flags: Model_1BP_Best

MC.11 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.11	393	11	22.372168	NaN	NaN	NaN	*	*	*
LB.1	1128	12	21.979768	-5.874261	49.748522	1.491317e+04	*	*
LB.1.7.2	87	11	13.599679	-30.758253	99.516507	2.323549e-07		*
KP.2.8	51	6	13.418012	-26.240827	90.481654	2.133845e-05	*
JN.1.42.2	28	6	13.024106	-26.548115	91.096230	1.565062e-05	*
MC.10.1.7	11	6	12.932207	-31.500739	101.001478	1.108597e-07
JN.1.30	57	12	12.876348	-14.976794	67.953588	1.665291e+00	*	*
MH.1	51	6	12.808788	-26.808743	91.617486	1.206744e-05	*
JN.1.15	42	11	12.200034	-25.653108	89.306216	3.830232e-05	*	*
KS.1.1.2	252	13	11.998422	-5.854720	49.709441	1.521444e+04	*

|||||

XFJ.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	18	180.312387	NaN	NaN	NaN	*	*	*
LF.7.9	20	30	176.417928	172.803235	-35.606470	5.503259e-04	*
XFJ.3	14	18	172.658536	172.658536	-35.317072	4.760441e-04	*	*
JN.1.4	8971	15	151.567214	148.522050	12.955900	1.562350e-14
JN.1	17255	18	141.621231	141.621231	26.757538	1.574514e-17		*
LF.7.1	165	30	140.788276	131.498824	47.002353	6.339957e-22
LF.7.9.1	48	30	135.667219	123.429237	63.141525	1.983033e-25
PY.2	17	30	134.235975	121.997992	66.004015	4.745574e-26
LF.7	58	30	129.168167	125.536082	58.927836	1.627495e-24
LF.7.2.1	67	30	128.107073	124.492380	61.015240	5.723768e-25

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2003_C|T, 2036_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3784_C|T, 3924_C|T, 3964_A|G, 4184_G|A, 4321_C|T, 4369_T|C, 6183_A|G, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10954_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 16741_G|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20384_C|T, 20796_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25494_G|A, 25584_C|T, 25599_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28093_C|T, 28144_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C,
29734_29759

 Case 11 (XFP): USA/NJ-GBW-GKISBBBF09579/2025



Target: 9 samples          Number of changes: 152                                                 
BC: MC.17.1 + XFJ.1        BC BR: 17-18                   BC BR coord: 5240 - 5241         
Direction L1: <<           Initial region span: 1-6,18-152 Gap history (edge excluded): 6-18
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  -                                                                             
Rec. model vs L1: 3.65e-182 Rec. model vs L2: 5.83e-26                                             
Flags: Model_2BP_Bad_L1_opp

MC.17.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.17.1	10	6	16.193570	NaN	NaN	NaN	*	*	*
KP.3.2.5	93	6	13.633444	-41.161875	126.323750	2.035376e-08		*
MC.9	298	6	12.481026	-16.429015	76.858029	1.118787e+03	*	*
MC.28.1.1	129	6	9.974781	-29.568854	103.137708	2.198456e-03	*	*
KP.2.3	4440	6	9.784386	-10.767208	65.534415	3.228684e+05	*	*
KP.3.1.1	12013	6	8.740606	-12.024975	68.049950	9.158291e+04	*	*
JN.1	17255	6	6.960903	-6.647399	57.294798	1.987553e+07	*	*
JN.1.4	8971	5	6.391498	-4.224472	52.448944	2.235174e+08	*	*
BA.2.6	424	5	3.268319	-73.506090	191.012180	1.825533e-22		*
FL.2.3	614	3	2.883722	-74.648894	193.297789	5.809283e-23

|||||

XFJ.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	18	188.148415	NaN	NaN	NaN	*	*	*
LF.7.9	20	30	183.528825	179.914132	-43.828264	2.652070e-04	*
XFJ.3	14	18	181.358668	181.358668	-46.717337	1.124969e-03	*	*
JN.1.4	8971	9	165.815847	154.198007	7.603986	1.801782e-15
LF.7.1	165	30	147.236797	137.947345	40.105310	1.571251e-22
LF.7.9.1	48	30	142.102988	129.865006	56.269988	4.865709e-26
PY.2	17	30	140.933038	128.695056	58.609887	1.510155e-26
LF.7.9.3	20	30	139.066797	129.102994	57.794013	2.275529e-26
LF.7	58	30	135.678767	132.046682	51.906635	4.304355e-25
LF.7.2.1	67	30	134.709279	131.094586	53.810828	1.664671e-25

Target sequence

, 21_C|T, 44_C|T, 198_G|A, 241_C|T, 670_T|G, 897_C|A, 1636_G|C, 2135_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3784_C|T, 4184_G|A, 4321_C|T, 4369_T|C, 5192_C|T, 6183_A|G, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10954_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20384_C|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C,
22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22991_A|G, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T,
25000_C|T, 25207_C|T, 25494_G|A, 25584_C|T, 25599_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28093_C|T, 28144_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 11 (XFP): USA/NY-GBW-GKISBBBE99208/2025



Target: 9 samples          Number of changes: 151                                                       
BC: XFJ.1 + MC.13          BC BR: 120-121                    BC BR coord: 25216 - 25217          
Direction L1: >>           Initial region span: 1-120,124-151 Gap history (edge excluded): 120-124
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 5.32e-45 Rec. model vs L2: 8.98e-170                                                  
Flags: Model_2BP_Bad_L1_opp

XFJ.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	120	207.715389	NaN	NaN	NaN	*	*	*
XFJ.3	14	120	193.289360	193.289360	-106.578720	5.436284e-07		*
LF.7.9	20	138	189.949082	180.922708	-81.845416	2.318733e-12
JN.1.4	8971	138	167.226103	139.783746	0.432507	3.150474e-30
LF.7	58	138	158.650769	149.236671	-18.473342	4.003674e-26
JN.1	17255	138	145.582746	117.749364	44.501271	8.485881e-40
LF.7.2.1	67	138	145.143356	135.707994	8.584012	5.353352e-32
KP.2.3	4440	138	141.800275	128.625518	22.748964	4.483833e-35
LF.7.1	165	139	141.496991	131.908981	16.182039	1.197586e-33
LF.7.1.2	26	138	139.200545	129.677247	20.645505	1.281323e-34

|||||

MC.13 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.13	807	124	32.600488	NaN	NaN	NaN	*	*	*
JN.1.7.5	427	122	31.495733	14.388791	41.222418	2.787095e+00	*
MC.2	396	124	31.383899	12.146246	45.707507	2.952302e-01	*	*
KP.3.1	1957	124	28.117999	8.880347	52.239306	1.127689e-02	*	*
KP.3.1.1	12013	122	26.714901	26.441947	17.116106	4.768704e+05	*
JN.1.42	494	124	23.359133	4.121480	61.757040	9.659341e-05	*	*
LB.1.3.2	390	124	23.315157	-2.179318	74.358636	1.773749e-07		*
JN.1.4.5	1757	124	22.606494	3.368273	63.263454	4.562750e-05	*	*
LB.1	1128	121	21.952824	21.952824	26.094351	5.377614e+03	*
JN.1.46	308	122	21.020620	11.020620	47.958761	9.584720e-02	*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2172_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3784_C|T, 4184_G|A, 4321_C|T, 4369_T|C, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10954_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 13427_G|A, 14408_C|T,
15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20384_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C,
22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T,
25207_C|T, 25494_G|A, 25584_C|T, 25599_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28093_C|T, 28144_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759, 29789_29790

 Case 11 (XFP): USA/NY-GBW-GKISBBBE99384/2025



Target: 9 samples          Number of changes: 150                                                       
BC: XFJ.3 + MC.13          BC BR: 119-120                    BC BR coord: 25216 - 25217          
Direction L1: >>           Initial region span: 1-119,123-150 Gap history (edge excluded): 119-123
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 2.02e-47 Rec. model vs L2: 2.13e-163                                                  
Flags: Model_2BP_Bad_L1_opp

XFJ.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.3	14	119	189.742002	NaN	NaN	NaN	*	*	*
XFJ.1	59	119	189.367704	189.367704	-92.735408	6.907343e-01	*	*
LF.7.9	20	137	186.401724	177.375350	-68.750700	4.265292e-06
JN.1.4	8971	137	161.828990	134.386633	17.226734	9.112320e-25
JN.1	17255	137	140.350729	112.517347	60.965305	2.894734e-34
LF.7	58	137	140.286584	130.872487	24.255027	2.710715e-26
KP.2.3	4440	137	134.856598	121.681841	42.636318	2.766416e-30
LF.7.2.1	67	137	126.600956	117.165593	51.668814	3.027457e-32
LF.7.9.3	20	137	125.528831	122.916078	40.167845	9.511987e-30
LF.7.1	165	138	123.657091	114.069080	57.861840	1.370682e-33

|||||

MC.13 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.13	807	123	32.600488	NaN	NaN	NaN	*	*	*
JN.1.7.5	427	121	31.495733	14.388791	41.222418	2.787095e+00	*
MC.2	396	123	31.383899	12.146246	45.707507	2.952302e-01	*	*
KP.3.1	1957	123	28.117999	8.880347	52.239306	1.127689e-02	*	*
KP.3.1.1	12013	121	26.714901	26.441947	17.116106	4.768704e+05	*
JN.1.42	494	123	23.359133	4.121480	61.757040	9.659341e-05	*	*
LB.1.3.2	390	123	23.315157	-2.179318	74.358636	1.773749e-07		*
JN.1.4.5	1757	123	22.606494	3.368273	63.263454	4.562750e-05	*	*
LB.1	1128	120	21.952824	21.952824	26.094351	5.377614e+03	*
JN.1.46	308	121	21.020620	11.020620	47.958761	9.584720e-02	*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2172_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3784_C|T, 4184_G|A, 4321_C|T, 4369_T|C, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10954_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20384_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C,
21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21995_21997, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T,
25494_G|A, 25584_C|T, 25599_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28093_C|T, 28144_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759, 29789_29790

 Case 11 (XFP): USA/NY-GBW-GKISBBBF41177/2025



Target: 9 samples         Number of changes: 150                                                       
BC: XFJ.3 + KP.3.1        BC BR: 119-120                    BC BR coord: 25216 - 25217          
Direction L1: >>          Initial region span: 1-119,123-150 Gap history (edge excluded): 119-123
Alt. candidates: [], []                                                                                       
Model 1BP/2BP comparison: 1BP vs 2BP: 7.95e-09                                                                
Rec. model vs L1: 3.48e-47 Rec. model vs L2: 5.92e-98                                                   
Flags: Model_1BP_Best

XFJ.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.3	14	119	180.460350	NaN	NaN	NaN	*	*	*
XFJ.1	59	119	179.256731	179.256731	-64.513463	2.996920e-01	*	*
LF.7.9	20	137	175.530838	166.504463	-39.008926	8.698022e-07
JN.1.4	8971	138	154.716590	126.066787	41.866426	2.379861e-24
JN.1	17255	137	146.673059	118.839678	56.320645	1.732902e-27
LF.7.9.3	20	111	132.756853	124.934294	44.131412	7.687744e-25
KP.2.3	4440	138	131.980467	118.341840	57.316320	1.051058e-27
LF.7	58	137	128.850800	119.436702	55.126596	3.141805e-27
LF.7.9.1	48	111	117.731415	109.908855	74.182289	2.293635e-31
JN.1.16.1	466	137	116.962133	107.671266	78.657468	2.441769e-32

|||||

KP.3.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1	1957	123	38.014816	NaN	NaN	NaN	*	*	*
KP.3.1.1	12013	121	35.490289	35.217335	-4.434669	1.379753e+07	*
LB.1	1128	120	35.345047	35.345047	-4.690094	1.571302e+07	*
MC.6	366	123	32.529829	13.292177	39.415647	4.148535e-03	*	*
JN.1.7.5	427	121	31.495733	14.388791	37.222418	1.246289e-02	*
MC.2	396	123	31.383899	12.146246	41.707507	1.320163e-03	*	*
JN.1.4	8971	123	28.351818	27.105650	11.788700	4.146418e+03	*	*
KP.2	1589	123	27.806551	8.568899	48.862202	3.698493e-05	*	*
KP.2.3	4440	123	27.553370	11.997640	42.004721	1.141970e-03	*	*
JN.1	17255	123	24.788840	24.026217	17.947565	1.905663e+02	*	*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3784_C|T, 4184_G|A, 4321_C|T, 4369_T|C, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10260_A|G, 10447_G|A, 10449_C|A, 10954_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 13944_C|T, 14408_C|T,
15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20384_C|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23896_C|T, 23933_A|G, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25494_G|A,
25584_C|T, 25599_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
27916_G|T, 28093_C|T, 28144_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 11 (XFP): IGS-10285-CVDP-7DC538F8-A098-480C-A770-7BD46A9127F9



Target: 9 samples          Number of changes: 153                                                 
BC: JN.1.48 + XFJ.1        BC BR: 14-15                   BC BR coord: 5240 - 5241         
Direction L1: <<           Initial region span: 1-8,18-153 Gap history (edge excluded): 8-18
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  1BP vs 2BP: 4.71e-02                                                          
Rec. model vs L1: 2.36e-104 Rec. model vs L2: 2.57e-25                                             
Flags: Model_1BP_Best

JN.1.48 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.48	10	8	19.331200	NaN	NaN	NaN	*	*	*
KP.2.2	1334	8	19.153903	-9.116624	48.233249	1.214897e+04	*	*
JN.1.11.1	226	8	17.701017	-20.165488	70.330976	1.930126e-01	*	*
LF.1.1.1	109	8	17.561244	-29.329905	88.659811	2.019652e-05	*	*
KP.2	1589	9	17.523915	-10.334275	50.668550	3.586744e+03	*	*
LB.1.3	778	9	16.123190	-11.732524	53.465048	8.844801e+02	*	*
JN.1	17255	12	14.074274	3.940983	22.118035	5.678767e+09	*
KP.3.1	1957	8	13.961572	-23.895152	77.790304	4.630919e-03	*	*
KP.2.3	4440	8	13.190259	-5.460208	40.920415	4.697707e+05	*	*
KP.3.1.1	12013	8	12.183771	-15.791870	61.583740	1.533289e+01	*	*

|||||

XFJ.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	18	176.702596	NaN	NaN	NaN	*	*	*
LF.7.9	20	29	176.417928	152.803235	8.393530	5.503259e-04	*
XFJ.3	14	18	169.048745	152.658536	8.682928	4.760441e-04	*	*
JN.1.4	8971	18	156.153465	139.759683	34.480634	1.189182e-09		*
LF.7.1	165	29	140.788276	111.498824	91.002353	6.339957e-22
LF.7.9.1	48	29	135.667219	103.429237	107.141525	1.983033e-25
PY.2	17	29	134.235975	101.997992	110.004015	4.745574e-26
LF.7	58	29	129.168167	105.536082	102.927836	1.627495e-24
JN.1	17255	18	128.113898	122.305365	69.389270	3.123476e-17		*
LF.7.2.1	67	29	128.107073	104.492380	105.015240	5.723768e-25

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2745_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3784_C|T, 3785_T|C, 4184_G|A, 4321_C|T, 4369_T|C, 4618_C|T, 6183_A|G, 6885_G|T, 7358_A|G, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10954_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18177_T|C, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20384_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24990_C|T, 25000_C|T, 25207_C|T, 25494_G|A, 25584_C|T, 25599_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28093_C|T, 28144_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29466_C|T, 29510_A|C, 29734_29759

 Case 25 (XDY): USA/NY-PRL-250401_81E07/2025



Target: 220 samples        Number of changes: 139                                               
BC: XDY.6 + CK.2           BC BR: 134-135                    BC BR coord: 28958 - 28959  
Direction L1: >>           Initial region span: 1-134,135-139 Gap history (edge excluded):
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 6.18e-22 Rec. model vs L2: 0.00e+00                                           
Flags: Model_2BP_Bad_L1_opp

XDY.6 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XDY.6	11	134	237.235060	NaN	NaN	NaN	*	*	*
XDY.5	17	134	237.107812	237.107812	-176.215624	8.824969e-01	*	*
XDY.7	10	134	229.329634	229.329634	-160.659269	3.688944e-04	*	*
LB.1.2.1	155	134	227.886172	227.886172	-157.772344	8.696542e-05	*	*
XDY.3	16	134	207.303742	207.303742	-116.607483	1.003613e-13		*
LB.1.1	52	134	198.644565	198.644565	-99.289130	1.740107e-17		*
KP.2	1589	134	194.385261	194.385261	-90.770521	2.457432e-19		*
LB.1.3	778	134	191.696262	191.696262	-85.392523	1.668128e-20		*
KP.3.2	737	134	189.475062	189.475062	-80.950123	1.811739e-21		*
LB.1.2	199	134	189.410463	189.410463	-80.820926	1.697721e-21		*

|||||

CK.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
CK.2	112	135	13.286246	NaN	NaN	NaN	*	*	*
KP.3.2.4	444	135	7.789327	7.789327	-5.578654	4.107256e-03	*	*
BV.1	84	137	6.868162	-13.131838	36.263675	3.373737e-12
KP.3.2.3	759	136	6.782703	6.535354	-3.070709	1.170880e-03	*	*
LF.7.1.6	14	137	6.514966	-13.485034	36.970069	2.365575e-12
BQ.1.25	479	136	6.009363	-3.990637	17.981274	3.144581e-08		*
XBB.1.5.89	23	137	5.870399	-14.129601	38.259203	1.241129e-12
BF.15	143	137	5.863296	-14.136704	38.273409	1.234938e-12
PD.2.1	10	137	5.619294	-14.380706	38.761412	9.665919e-13
CM.10	43	137	5.449335	-14.550665	39.101330	8.154796e-13

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5284_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T,
10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19669_G|A,
19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21633_21641, 21653_21655, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22111_G|T,
22131_G|C, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22332_G|T, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A,
22786_A|C, 22813_G|T, 22858_C|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24700_C|T, 24872_G|T, 24990_C|T, 25000_C|T, 25081_T|C, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T,
26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29284_C|T, 29383_G|A, 29466_C|T,
29510_A|C, 29734_29759

 Case 46 (XFJ): OZ262381



Target: 24 samples         Number of changes: 146                                                 
BC: JN.1.53 + XFJ.1        BC BR: 11-12                   BC BR coord: 4839 - 4840         
Direction L1: <<           Initial region span: 1-9,12-146 Gap history (edge excluded): 9-12
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  1BP vs 2BP: 5.13e-02                                                          
Rec. model vs L1: 1.29e-158 Rec. model vs L2: 3.31e-16                                             
Flags: Model_1BP_Best

JN.1.53 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.53	62	9	15.728510	NaN	NaN	NaN	*	*	*
LF.7.9.3	20	5	11.825673	5.189982	25.620036	1.246501e-04	*
XFB.3	56	5	11.670112	4.885385	26.229230	9.188250e-05	*
XEL.5	19	5	11.593891	-15.870858	67.741715	8.901246e-14
LC.1	10	5	11.297148	-2.806209	41.612418	4.202505e-08
XEC.35.1	28	5	11.252812	-1.779095	39.558190	1.171278e-07
LF.7.1.11	20	5	11.163617	-8.501504	53.003008	1.413192e-10
XEC.4.7	13	5	11.141517	-1.741355	39.482709	1.219079e-07
KP.2.3	4440	9	11.116294	9.606882	16.786236	1.030630e-02	*	*
XEC.23	142	5	11.050090	-1.999132	39.998263	9.399728e-08

|||||

XFJ.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	12	309.884615	NaN	NaN	NaN	*	*	*
XFJ.3	14	12	289.265270	283.628835	-263.257669	3.959117e-12		*
LF.7.9	20	7	259.623071	256.376545	-208.753090	5.766367e-24
LF.7.2.1	67	7	196.506412	193.350209	-82.700418	2.451842e-51
LF.7.9.3	20	29	191.091612	185.303736	-66.607472	7.863094e-55
PC.3	42	7	188.249405	185.108240	-66.216481	6.470026e-55
LF.7.9.1	48	29	185.630105	177.546997	-51.093994	3.353268e-58
PY.2	17	29	185.498143	177.436089	-50.872177	3.003972e-58
LF.7	58	7	183.108050	179.931167	-55.862333	3.641335e-57
PC.3.1	27	7	180.683815	177.542650	-51.085300	3.353268e-58

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2308_T|C, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10273_T|C, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11812_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20799_T|C, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T,
25844_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A, 27807_C|T, 27810_T|C,
28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 46 (XFJ): OZ276211



Target: 24 samples         Number of changes: 147                                                 
BC: LP.8.1 + XFJ.1         BC BR: 12-13                   BC BR coord: 4839 - 4840         
Direction L1: <<           Initial region span: 1-6,13-147 Gap history (edge excluded): 6-13
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  1BP vs 2BP: 9.83e-02                                                          
Rec. model vs L1: 2.11e-186 Rec. model vs L2: 2.67e-06                                             
Flags: Model_1BP_Best

LP.8.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LP.8.1	1124	6	12.349269	NaN	NaN	NaN	*	*	*
LF.7.9.3	20	5	11.825673	-4.810018	53.620036	2.328374e-02	*	*
XFB.3	56	5	11.670112	-5.114615	54.229230	1.716299e-02	*	*
XEL.5	19	5	11.593891	-25.870858	95.741715	1.662689e-11		*
LC.1	10	5	11.297148	-12.806209	69.612418	7.849977e-06		*
XEC.35.1	28	5	11.252812	-11.779095	67.558190	2.187863e-05	*	*
LF.7.1.11	20	5	11.163617	-18.501504	81.003008	2.639741e-08		*
XEC.4.7	13	5	11.141517	-11.741355	67.482709	2.277152e-05	*	*
XEC.23	142	5	11.050090	-11.999132	67.998263	1.755802e-05	*	*
LD.1.1	11	5	10.972996	-24.599596	93.199192	5.920590e-11		*

|||||

XFJ.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	13	309.884615	NaN	NaN	NaN	*	*	*
XFJ.3	14	13	289.265270	283.628835	-263.257669	3.959117e-12		*
LF.7.9	20	8	259.623071	256.376545	-208.753090	5.766367e-24
LF.7.2.1	67	8	196.506412	193.350209	-82.700418	2.451842e-51
LF.7.9.3	20	30	191.091612	185.303736	-66.607472	7.863094e-55
PC.3	42	8	188.249405	185.108240	-66.216481	6.470026e-55
LF.7.9.1	48	30	185.630105	177.546997	-51.093994	3.353268e-58
PY.2	17	30	185.498143	177.436089	-50.872177	3.003972e-58
LF.7	58	8	183.108050	179.931167	-55.862333	3.641335e-57
PC.3.1	27	8	180.683815	177.542650	-51.085300	3.353268e-58

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1173_T|C, 2308_T|C, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10273_T|C, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11812_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20799_T|C, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C,
21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T,
25584_C|T, 25844_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A, 27807_C|T,
27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 46 (XFJ): OZ276211



Target: 24 samples         Number of changes: 147                                                 
BC: LP.8.1 + XFJ.1         BC BR: 12-13                   BC BR coord: 4839 - 4840         
Direction L1: <<           Initial region span: 1-6,13-147 Gap history (edge excluded): 6-13
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  1BP vs 2BP: 9.83e-02                                                          
Rec. model vs L1: 2.11e-186 Rec. model vs L2: 2.67e-06                                             
Flags: Model_1BP_Best

LP.8.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LP.8.1	1124	6	12.349269	NaN	NaN	NaN	*	*	*
LF.7.9.3	20	5	11.825673	-4.810018	53.620036	2.328374e-02	*	*
XFB.3	56	5	11.670112	-5.114615	54.229230	1.716299e-02	*	*
XEL.5	19	5	11.593891	-25.870858	95.741715	1.662689e-11		*
LC.1	10	5	11.297148	-12.806209	69.612418	7.849977e-06		*
XEC.35.1	28	5	11.252812	-11.779095	67.558190	2.187863e-05	*	*
LF.7.1.11	20	5	11.163617	-18.501504	81.003008	2.639741e-08		*
XEC.4.7	13	5	11.141517	-11.741355	67.482709	2.277152e-05	*	*
XEC.23	142	5	11.050090	-11.999132	67.998263	1.755802e-05	*	*
LD.1.1	11	5	10.972996	-24.599596	93.199192	5.920590e-11		*

|||||

XFJ.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	13	309.884615	NaN	NaN	NaN	*	*	*
XFJ.3	14	13	289.265270	283.628835	-263.257669	3.959117e-12		*
LF.7.9	20	8	259.623071	256.376545	-208.753090	5.766367e-24
LF.7.2.1	67	8	196.506412	193.350209	-82.700418	2.451842e-51
LF.7.9.3	20	30	191.091612	185.303736	-66.607472	7.863094e-55
PC.3	42	8	188.249405	185.108240	-66.216481	6.470026e-55
LF.7.9.1	48	30	185.630105	177.546997	-51.093994	3.353268e-58
PY.2	17	30	185.498143	177.436089	-50.872177	3.003972e-58
LF.7	58	8	183.108050	179.931167	-55.862333	3.641335e-57
PC.3.1	27	8	180.683815	177.542650	-51.085300	3.353268e-58

Target sequence

 Case 46 (XFJ): OZ280587



Target: 24 samples         Number of changes: 144                                             
BC: JN.1.8.1 + XFJ.1       BC BR: 11-12                    BC BR coord: 4839 - 4840    
Direction L1: <<           Initial region span: 1-11,12-144 Gap history (edge excluded):
Alt. candidates: [], []                                                                              
Model 1BP/2BP comparison:  1BP vs 2BP: 7.19e-05                                                      
Rec. model vs L1: 4.87e-121 Rec. model vs L2: 3.58e-21                                         
Flags: Model_1BP_Best

JN.1.8.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.8.1	1498	11	18.509376	NaN	NaN	NaN	*	*	*
XDY.3	16	8	17.874592	10.021450	3.957100	2.055133e-04	*
MC.11.3	19	8	17.009594	9.156452	5.687095	8.653168e-05	*
MC.24.1	25	8	16.694335	8.841193	6.317613	6.314986e-05	*
KP.3.7	29	8	16.407356	8.554214	6.891573	4.748959e-05	*
LQ.1.2	32	8	16.325319	8.472177	7.055646	4.361977e-05	*
KP.2.11	40	8	16.161874	8.308732	7.382535	3.717032e-05	*
JN.1.50.1	48	8	16.040725	2.458124	19.083752	1.070468e-07
JN.10	47	8	16.037928	8.184786	7.630429	3.280269e-05	*
KP.2.1	47	8	15.952397	8.077749	7.844503	2.953307e-05	*

|||||

XFJ.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	12	292.083200	NaN	NaN	NaN	*	*	*
XFJ.3	14	12	285.078963	279.442528	-246.885056	3.239797e-06		*
LF.7.9	20	3	243.082377	238.009337	-164.018673	3.277373e-24
LF.7.2.1	67	3	181.001759	175.930259	-39.860518	3.585291e-51
PC.3	42	10	169.389947	167.243089	-22.486178	6.062851e-55
LF.7	58	3	167.259247	162.151348	-12.302696	3.714895e-57
LF.7.1	165	3	167.247168	146.263393	19.473214	4.690063e-64
PC.4	10	3	166.103443	160.925043	-9.850086	1.091279e-57
LF.7.9.3	20	3	164.047104	159.091847	-6.183695	1.741828e-58
PY.1	82	12	161.490050	161.490050	-10.980101	1.920048e-57		*

Target sequence

, 241_C|T, 519_524, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3876_C|T, 4184_G|A, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11893_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C,
17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20799_T|C, 21610_.|ATGCCGCTGTTT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23063_A|T, 23075_T|C, 23156_A|G, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25844_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C

 Case 46 (XFJ): USA/CA-CDPH-6000021782/2025



Target: 24 samples         Number of changes: 146                                               
BC: LP.8.1 + XFJ.1         BC BR: 4-5                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-4,7-146 Gap history (edge excluded): 4-7
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 1.50e-192 Rec. model vs L2: 1.55e-06                                           
Flags: Model_2BP_Bad_L1_opp

LP.8.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LP.8.1	1124	4	7.743010	NaN	NaN	NaN	*	*	*
MC.2	396	4	7.408891	7.408891	-4.817781	7.153381e-01	*	*
NY.13	463	4	7.221759	7.221759	-4.443517	5.915554e-01	*	*
KP.3	769	4	6.727092	6.727092	-3.454184	3.605949e-01	*	*
XBB.1.32	20	3	6.598157	-3.401843	16.803687	1.444734e-05	*	*
BA.5.2.44	120	3	5.006053	-4.993947	19.987895	2.931489e-06		*
BU.3	122	3	4.981293	-5.018707	20.037414	2.859110e-06		*
BT.2	227	3	4.355290	-5.644710	21.289419	1.530372e-06		*
BA.5.1.25	1675	3	4.146734	-5.853266	21.706533	1.240495e-06		*
BN.1.7	382	3	3.848124	-6.151876	22.303753	9.235878e-07		*

|||||

XFJ.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	7	302.669687	NaN	NaN	NaN	*	*	*
XFJ.3	14	7	290.757786	270.757786	-213.515571	6.722839e-06		*
LF.7.9	20	7	250.882577	230.882577	-133.765154	3.236386e-23		*
LF.7.2.1	67	7	189.402513	169.402513	-10.805027	6.451126e-50		*
PC.3	42	7	180.669337	151.943580	24.112839	1.685986e-57		*
LF.7	58	7	175.624961	155.624961	16.750078	6.684325e-56		*
PC.4	10	7	174.442640	154.442640	19.114720	2.053951e-56		*
PC.3.1	27	7	171.865144	143.153030	41.693940	2.566879e-61		*
LF.7.9.1	48	7	168.444888	139.395996	49.208009	5.976654e-63		*
PY.2	17	7	167.291545	130.504058	66.991884	8.233418e-67		*

Target sequence

, 241_C|T, 670_T|G, 709_G|T, 897_C|A, 1042_G|A, 1919_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C,
17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20470_C|A, 20799_T|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|A, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T,
25844_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A, 27768_27772, 27807_C|T,
27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C

 Case 46 (XFJ): USA/CA-LACPHL-AY11911/2025



Target: 24 samples        Number of changes: 149                                             
BC: JN.1 + XFJ.1          BC BR: 29-30                    BC BR coord: 12771 - 12772  
Direction L1: <<          Initial region span: 1-29,30-149 Gap history (edge excluded):
Alt. candidates: [], []                                                                             
Model 1BP/2BP comparison: 1BP vs 2BP: 3.97e-15                                                      
Rec. model vs L1: 5.60e-82 Rec. model vs L2: 5.00e-29                                         
Flags: Model_1BP_Best

JN.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1	17255	29	36.851243	NaN	NaN	NaN	*	*	*
JN.1.4	8971	29	33.928911	33.928911	-3.857822	5.393369e-02	*	*
KP.3.1.1	12013	29	22.001203	16.667411	30.665177	1.713034e-09		*
MC.13	807	26	21.562333	10.652758	42.694485	4.203936e-12
JN.1.16.1	466	24	16.808532	4.776861	54.446278	1.174910e-14
JN.1.7	1974	24	15.175852	3.106624	57.786753	2.211733e-15
MC.19	221	24	13.940467	-3.367814	70.735628	3.409384e-18
KP.2	1589	24	12.301415	10.802039	42.395921	4.859916e-12
KP.3.3	1715	24	11.826561	11.386676	41.226649	8.723505e-12
KP.1.1.1	578	24	11.276705	-0.737140	65.474279	4.753811e-17

|||||

XFJ.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	30	267.083694	NaN	NaN	NaN	*	*	*
XFJ.3	14	6	246.814578	238.860040	-211.720079	5.521261e-13
LF.7.9	20	28	223.053004	218.611015	-171.222030	8.862882e-22
LF.7.2.1	67	28	160.026668	155.599717	-45.199433	3.825425e-49
JN.1.4	8971	4	159.058345	120.094623	25.810754	1.455640e-64
LF.7.9.3	20	28	158.329306	153.887317	-41.774634	6.884377e-50
LF.7.9.1	48	28	152.867799	148.425810	-30.851619	2.928308e-52
PY.2	17	28	152.735837	148.293848	-30.587696	2.571334e-52
PC.3	42	28	151.784699	147.342710	-28.685420	9.944403e-53
LF.7.1	165	28	148.980463	144.556823	-23.113646	6.107973e-54

Target sequence

, 222, 241_C|T, 670_T|G, 897_C|A, 1158_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5239_C|T, 6183_A|G, 7482_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10681_C|T, 11042_G|T, 11094_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|G, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20799_T|C, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C,
21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T,
25584_C|T, 25844_C|T, 25919_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A,
27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29690_G|T, 29734_29759

 Case 46 (XFJ): USA/MA-MASPHL-14074/2025



Target: 24 samples         Number of changes: 150                                               
BC: JN.1 + XFJ.1           BC BR: 5-6                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-5,7-150 Gap history (edge excluded): 5-7
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 3.72e-59 Rec. model vs L2: 1.13e-09                                           
Flags: Model_2BP_Bad_L1_opp

JN.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1	17255	5	2.994024	NaN	NaN	NaN	*	*	*
BA.4	10442	4	1.503026	-12.358458	36.716916	2.144906e-07		*
BA.4.6	19369	4	0.776654	-13.122193	38.244386	1.003100e-07		*

|||||

XFJ.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	7	280.438942	NaN	NaN	NaN	*	*	*
XFJ.3	14	7	275.318741	265.318741	-200.637483	5.976023e-03	*	*
LF.7.9	20	7	245.718955	235.718955	-141.437910	8.342488e-16		*
PC.3	42	7	174.780514	156.054758	17.890485	2.104872e-50		*
LF.7.2.1	67	7	173.494668	163.494668	3.010665	3.584071e-47		*
LF.7.9.1	48	22	166.461577	143.507920	42.984160	7.498966e-56
LF.7	58	7	159.967518	149.967518	30.064964	4.792297e-53		*
PC.4	10	7	158.792875	148.792875	32.414250	1.479952e-53		*
LF.7.1	165	7	158.231093	148.231093	33.537813	8.411460e-54		*
PC.3.1	27	7	156.272177	137.560064	54.879872	1.954111e-58		*

Target sequence

, 241_C|T, 492_C|T, 580_T|C, 670_T|G, 897_C|A, 1851_T|C, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 9907_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12253_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16600_T|C, 17410_C|T, 18129_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20799_T|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C,
22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T,
25207_C|T, 25584_C|T, 25844_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A,
27807_C|T, 27810_T|C, 27970_C|T, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29700_A|G, 29734_29759

 Case 46 (XFJ): IGS-10285-CVDP-2AAB5C9E-0709-4787-8906-A3F7486EE388



Target: 24 samples        Number of changes: 148                                                               
BC: XFJ.1 + LF.7 + XFJ.1  BC BR: 9-10, 13-14                   BC BR coord: 4330 - 4331, 7841 - 7842    
Direction L1: <<          Initial region span: 1-9,11-13,14-148 Gap history (edge excluded): 9-14 -> 9-11
Alt. candidates: [], []                                                                                               
Model 1BP/2BP comparison: 2BP vs 1BP: 5.37e-04                                                                        
Rec. model vs L1: 7.78e-16 Rec. model vs L2: 1.36e-87                                                           
Flags: Model_2BP_Best

XFJ.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	9	15.114291	None	None	None	*	*	*

|||||

LF.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	11	12.675918	NaN	NaN	NaN	*	*	*
NL.4.1	26	12	9.730528	-10.269472	30.538945	2.388130e-06		*
JN.1.1.6	13	12	8.025780	-11.974220	33.948441	4.340961e-07		*
XEC.39	155	12	7.620273	-12.379727	34.759454	2.895320e-07		*
KS.1	505	11	7.545340	-2.454660	14.909319	5.916560e-03	*	*
EA.1	124	13	6.980938	-23.019062	56.038124	6.931118e-12
HF.1.1	292	13	6.980938	-30.070499	70.140998	6.012114e-15
EA.2	17	13	6.980938	-23.019062	56.038124	6.931118e-12
BA.5.2.35	1368	13	6.978010	-23.021990	56.043981	6.931118e-12
BQ.1.1.52	476	13	6.968253	-23.031747	56.063494	6.862152e-12

|||||

XFJ.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	14	290.448367	NaN	NaN	NaN	*	*	*
XFJ.3	14	14	270.809714	285.918573	-257.837145	2.939577e-09		*
LF.7.9	20	1	229.837314	240.081891	-166.163783	3.632669e-29
LF.7	58	1	182.882400	180.206482	-46.412964	3.604489e-55
LF.7.2.1	67	1	168.121624	178.366201	-42.732402	5.724557e-56
PC.3	42	17	158.301525	169.861290	-25.722580	1.158957e-59
LF.7.1	165	17	156.766308	168.301276	-22.602553	2.435387e-60
LF.7.9.1	48	20	156.736585	162.886795	-11.773590	1.083586e-62
PY.2	17	20	155.305341	161.498110	-8.996219	2.712473e-63
PC.4	10	1	153.511694	163.756271	-13.512543	2.586423e-62

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4665_G|A, 5239_C|T, 6183_A|G, 7006_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15250_A|G, 15714_C|T, 15756_T|A, 16600_T|C,
16605_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20799_T|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T,
25844_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A, 27807_C|T, 27810_T|C,
28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28419_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29296_C|T, 29510_A|C, 29734_29759

 Case 46 (XFJ): IGS-10285-CVDP-3BC3A18F-E0E3-415C-97ED-0C225785CACE



Target: 24 samples        Number of changes: 146                                                             
BC: XFJ.1 + KP.2.5 + XFJ.1 BC BR: 5-6, 11-12                   BC BR coord: 3037 - 3038, 5238 - 5239   
Direction L1: <<          Initial region span: 1-5,7-11,12-146 Gap history (edge excluded): 5-12 -> 5-7
Alt. candidates: [], []                                                                                             
Model 1BP/2BP comparison: 2BP vs 1BP: 2.32e-05                                                                      
Rec. model vs L1: 8.95e-16 Rec. model vs L2: 1.60e-202                                                        
Flags: Model_2BP_Best

XFJ.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	5	5.748333	None	None	None	*	*	*

|||||

KP.2.5 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.5	66	7	15.417185	NaN	NaN	NaN	*	*	*
JN.1.2	650	7	13.151366	3.151366	7.697269	1.038300e-01	*	*
AY.86	33	11	8.955276	-42.156247	98.312495	2.190844e-21
XBB.1.5.49	1290	9	5.238244	-24.761756	63.523513	7.855322e-14
BA.5.1.22	4997	9	4.571351	-20.370538	54.741077	6.334565e-12
BE.3	3742	9	4.169489	-25.830511	65.661022	2.694442e-14
AY.90	1220	11	3.841100	-41.691015	97.382029	3.487855e-21
B.1.241	765	11	3.614683	-36.560117	87.120234	5.895072e-19
BA.2.10	14971	9	3.478889	-26.521111	67.042222	1.351468e-14
BA.5.5	23560	9	3.428939	-9.117326	32.234652	4.894419e-07

|||||

XFJ.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	12	308.218988	NaN	NaN	NaN	*	*	*
XFJ.3	14	12	300.565137	306.365050	-304.730101	5.004514e-04	*	*
LF.7.9	20	12	254.759708	260.559622	-213.119243	6.404765e-24		*
LF.7.2.1	67	12	193.045558	198.753608	-89.507217	9.224286e-51		*
PC.3	42	12	184.457844	190.233660	-72.467319	1.839686e-54		*
LF.7	58	12	179.573872	185.356394	-62.712788	1.397612e-56		*
PC.4	10	12	178.328728	184.128641	-60.257282	4.105593e-57		*
LF.7.9.1	48	12	177.480758	183.238111	-58.476223	1.685986e-57		*
LF.7.1	165	12	176.386507	182.155876	-56.311752	5.696975e-58		*
PY.2	17	12	176.070566	181.870479	-55.740959	4.284207e-58		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3053_G|A, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5219_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T,
18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20799_T|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25844_C|T, 25919_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29690_G|T, 29734_29759

 Case 46 (XFJ): IGS-10285-CVDP-5C418B6D-4A8E-423C-9873-BB3B605DD9B9



Target: 24 samples        Number of changes: 146                                                                    
BC: XFJ.1 + GA.4.1 + XFJ.1 BC BR: 138-139, 140-141                   BC BR coord: 28361 - 28362, 28877 - 28878
Direction L1: >>          Initial region span: 1-138,139-140,141-146 Gap history (edge excluded): 138-141 ->  
Alt. candidates: [], []                                                                                                    
Model 1BP/2BP comparison: 2BP vs 1BP: 2.30e-01                                                                             
Rec. model vs L1: 1.15e-17 Rec. model vs L2: 0.00e+00                                                                
Flags: Model_2BP_Best

XFJ.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	138	307.554472	NaN	NaN	NaN	*	*	*
XFJ.3	14	138	302.378606	310.037560	-300.075121	6.313911e-03	*	*
LF.7.9	20	138	262.340879	269.837314	-219.674628	2.185188e-20		*
LF.7.2.1	67	138	210.988783	218.413337	-116.826673	1.018747e-42		*
LF.7	58	138	197.572545	205.122300	-90.244600	1.714437e-48		*
PC.3	42	146	192.777543	190.890956	-61.781913	1.132690e-54
LF.7.1	165	146	189.604172	189.067843	-58.135686	1.835249e-55
PC.4	10	138	185.958101	193.511694	-67.023388	1.555831e-53		*
PC.3.1	27	138	183.581089	191.163082	-62.326164	1.491221e-54		*
JN.1.4	8971	146	179.139713	178.456944	-36.913889	4.504629e-60

|||||

GA.4.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
GA.4.1	97	140	9.361926	NaN	NaN	NaN	*	*	*
B.1.1.528	51	140	9.361926	9.361926	-14.723851	1.000000	*	*
B.1.1.322	31	140	9.361926	9.361926	-14.723851	1.000000	*	*
C.37.1	77	140	9.268469	9.268469	-14.536938	0.913931	*	*
MC.1.4.1	41	140	9.156617	9.156617	-14.313235	0.814647	*	*
B.1.1.408	15	140	9.075724	9.075724	-14.151448	0.752014	*	*
XBB.3.1	13	140	8.390910	8.390910	-12.781820	0.379083	*	*
XBB.1.43.1	22	140	7.975631	7.975631	-11.951262	0.250324	*	*
FY.8.1	29	140	7.232504	7.232504	-10.465008	0.119433	*	*
FY.4.1	61	140	7.229223	7.229223	-10.458446	0.118837	*	*

|||||

XFJ.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	141	7.551709	None	None	None	*	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T,
10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 16887_C|T, 17410_C|T, 18163_A|G,
18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20799_T|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22093_G|C, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25844_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T,
28362_28370, 28877_A|T, 28878_G|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 46 (XFJ): IGS-10285-CVDP-945917A7-03F4-44B7-B15E-9DAC718B9032



Target: 24 samples        Number of changes: 146                                                                    
BC: XFJ.1 + GA.4.1 + XFJ.1 BC BR: 138-139, 140-141                   BC BR coord: 28361 - 28362, 28877 - 28878
Direction L1: >>          Initial region span: 1-138,139-140,141-146 Gap history (edge excluded): 138-141 ->  
Alt. candidates: [], []                                                                                                    
Model 1BP/2BP comparison: 2BP vs 1BP: 2.30e-01                                                                             
Rec. model vs L1: 1.15e-17 Rec. model vs L2: 0.00e+00                                                                
Flags: Model_2BP_Best

XFJ.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	138	307.554472	NaN	NaN	NaN	*	*	*
XFJ.3	14	138	302.378606	310.037560	-294.075121	6.313911e-03	*	*
LF.7.9	20	138	262.340879	269.837314	-213.674628	2.185188e-20		*
LF.7.2.1	67	138	200.697070	208.121624	-90.243247	3.443538e-47		*
PC.3	42	146	192.777543	190.890956	-55.781913	1.132690e-54
LF.7	58	138	187.136582	194.686337	-63.372674	5.038004e-53		*
PC.4	10	138	185.958101	193.511694	-61.023388	1.555831e-53		*
PC.3.1	27	138	183.581089	191.163082	-56.326164	1.491221e-54		*
LF.7.1	165	146	179.520565	178.984236	-31.968471	7.653060e-60
LF.7.9.1	48	138	170.950858	178.501748	-31.003495	4.711968e-60		*

|||||

GA.4.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
GA.4.1	97	140	9.361926	NaN	NaN	NaN	*	*	*
B.1.1.528	51	140	9.361926	9.361926	-14.723851	1.000000	*	*
B.1.1.322	31	140	9.361926	9.361926	-14.723851	1.000000	*	*
C.37.1	77	140	9.268469	9.268469	-14.536938	0.913931	*	*
MC.1.4.1	41	140	9.156617	9.156617	-14.313235	0.814647	*	*
B.1.1.408	15	140	9.075724	9.075724	-14.151448	0.752014	*	*
XBB.3.1	13	140	8.390910	8.390910	-12.781820	0.379083	*	*
XBB.1.43.1	22	140	7.975631	7.975631	-11.951262	0.250324	*	*
FY.8.1	29	140	7.232504	7.232504	-10.465008	0.119433	*	*
FY.4.1	61	140	7.229223	7.229223	-10.458446	0.118837	*	*

|||||

XFJ.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFJ.1	59	141	7.551709	None	None	None	*	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T,
10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G,
18894_C|T, 19955_C|T, 20055_A|G, 20799_T|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22093_G|C, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23728_T|C, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25844_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C,
28311_C|T, 28362_28370, 28877_A|T, 28878_G|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 52 (XES): USA/IVY-G25Y93M8/2025



Target: 59 samples             Number of changes: 152                                                            
BC: KP.3.3 + KP.2.3.15 + KP.3.3 BC BR: 11-12, 16-17                   BC BR coord: 4330 - 4331, 6470 - 6471
Direction L1: <<               Initial region span: 1-11,12-16,17-152 Gap history (edge excluded): 11-17 ->
Alt. candidates: [], []                                                                                                 
Model 1BP/2BP comparison:      2BP vs 1BP: 1.08e-10                                                                     
Rec. model vs L1: 9.36e-20     Rec. model vs L2: 4.00e-70                                                        
Flags: Model_2BP_Best

KP.3.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.3	1715	11	5.816434	None	None	None	*	*	*

|||||

KP.2.3.15 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3.15	59	16	13.298012	NaN	NaN	NaN	*	*	*
AY.70	861	12	5.662483	-41.890318	109.780635	1.074701e-24
FL.24	72	12	4.611686	-39.810180	105.620360	8.602409e-24
BF.7	11554	14	4.040111	-5.197174	36.394348	9.283753e-09
AA.5	52	12	3.797674	-47.083547	120.167094	5.958373e-27
AY.85	549	12	3.743404	-37.364394	100.728788	9.919050e-23
AY.127	7489	12	3.663016	-27.742787	81.485573	1.494111e-18
BA.2.52	379	13	3.469920	-26.530080	79.060159	5.035595e-18
NY.16.1	20	12	3.366891	-34.734554	95.469109	1.376146e-21
HY.1	179	13	3.221021	-26.778979	79.557958	3.921725e-18

|||||

KP.3.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.3	1715	17	208.255914	NaN	NaN	NaN	*	*	*
KP.3.1	1957	15	190.995817	178.431488	-20.862975	3.324640e-16
KP.3.1.1	12013	17	186.671839	192.864437	-49.728875	6.177113e-10		*
KP.2.3	4440	17	178.490339	173.622995	-11.245989	2.722449e-18		*
KP.3	769	17	157.248598	152.328392	31.343217	1.536946e-27		*
MC.24.1	25	17	155.723534	150.865679	34.268643	3.551545e-28		*
XEC.2	921	57	153.328110	147.582506	40.834988	1.336384e-29
MC.8.1	174	48	152.771335	125.120295	85.759410	2.341563e-39
PG.3	31	48	152.651791	122.567783	90.864434	1.828331e-40
KP.2	1589	17	150.262194	145.352550	45.294900	1.436993e-30		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1358_G|A, 1404_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4891_C|T, 5310_C|T, 6022_A|T, 6183_A|G, 6471_C|A, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 8836_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 17334_G|T, 17410_C|T, 17745_C|T, 18163_A|G, 18492_A|G, 18642_A|C, 18894_C|T, 19011_C|T, 19803_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21633_21641, 21653_21655, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22000_C|A, 22032_T|C, 22033_C|A, 22034_A|G, 22054_T|C, 22194_22196, 22200_T|G, 22208_C|T,
22225_G|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G,
22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23126_G|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T,
24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27373, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28093_C|T, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 55 (XEQ): USA/AR-CDC-2-8381796/2025



Target: 269 samples       Number of changes: 142                                                                  
BC: KP.2 + KP.3.1.1 + KP.2 BC BR: 10-11, 20-21                   BC BR coord: 6183 - 6184, 9533 - 9534      
Direction L1: <<          Initial region span: 1-10,13-20,21-142 Gap history (edge excluded): 10-21 -> 10-13
Alt. candidates: [], []                                                                                                  
Model 1BP/2BP comparison: 2BP vs 1BP: 1.83e-04                                                                           
Rec. model vs L1: 7.15e-28 Rec. model vs L2: 9.68e-29                                                              
Flags: Model_2BP_Best

KP.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2	1589	10	18.699517	None	None	None	*	*	*

|||||

KP.3.1.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.1	12013	13	12.244538	NaN	NaN	NaN	*	*	*
JN.1	17255	12	11.352938	11.157600	1.684800	2.351374e+00	*	*
JN.1.1	3081	13	10.526826	0.496192	23.007616	5.489985e-05	*	*
NL.15	13	17	10.497880	-22.343583	68.687166	6.611274e-15
KP.2.8	51	17	9.131004	-28.097270	80.194541	2.104224e-17
XBB.1.5.20	860	18	8.615822	-61.384178	146.768357	7.335481e-32
BR.5	15	18	8.615822	-70.278195	164.556391	1.005493e-35
BR.4	11	18	8.615822	-70.278195	164.556391	1.005493e-35
BR.1.2	119	18	8.615822	-70.278195	164.556391	1.005493e-35
BR.2.1	313	18	8.606222	-61.393778	146.787557	7.262492e-32

|||||

KP.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2	1589	21	216.533120	NaN	NaN	NaN	*	*	*
KP.3.1.1	12013	1	210.962964	200.660225	-111.320449	9.644246e-16
JN.1	17255	1	202.008374	190.850774	-91.701548	5.294676e-20
XEC.2	921	17	197.785733	212.810206	-135.620411	1.823670e-10
MC.24.1	25	39	196.620020	213.609804	-137.219608	4.058652e-10
KS.1.1.2	252	1	195.583419	205.072607	-120.145215	7.974040e-14
KP.3	769	17	188.912328	203.749124	-117.498247	2.119524e-14
XEK.5	28	21	186.525203	205.243853	-120.487706	9.451669e-14		*
XEC.9	305	17	186.478244	200.410249	-110.820498	7.510946e-16
XEK.1	88	21	185.726148	204.507477	-119.014953	4.509523e-14		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6701_C|T, 6989_T|C, 7842_A|G, 7936_G|A, 8293_C|T, 8386_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9532_C|T, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16887_C|T, 16943_G|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22546_A|G, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25163_C|A, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 55 (XEQ): USA/CA-CDPH-500146881/2025



Target: 269 samples       Number of changes: 135                                                               
BC: KP.2 + LF.7.1.4 + KP.2 BC BR: 8-9, 10-11                   BC BR coord: 6183 - 6184, 7118 - 7119     
Direction L1: <<          Initial region span: 1-8,9-10,12-135 Gap history (edge excluded): 8-12 -> 10-12
Alt. candidates: [], []                                                                                               
Model 1BP/2BP comparison: 2BP vs 1BP: 1.34e-08                                                                        
Rec. model vs L1: 2.65e-19 Rec. model vs L2: 6.49e-120                                                          
Flags: Model_2BP_Best

KP.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2	1589	8	9.339591	None	None	None	*	*	*

|||||

LF.7.1.4 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7.1.4	12	10	9.812013	NaN	NaN	NaN	*	*	*
BF.7.19	413	11	7.315788	2.329466	-0.658931	5.642574e-04	*	*
BA.5.1.31	43	9	5.680838	-4.319162	12.638323	7.301616e-07		*
XFH.2	15	9	5.680838	-4.319162	12.638323	7.301616e-07		*
XFH.1	10	9	5.680838	-4.319162	12.638323	7.301616e-07		*
LF.7.1.8	44	9	5.680838	-4.319162	12.638323	7.301616e-07		*
LF.7.1.5	40	9	5.680838	-4.319162	12.638323	7.301616e-07		*
LF.7.1.6	14	9	5.680838	-4.319162	12.638323	7.301616e-07		*
LF.7.1.10	13	9	5.680838	-4.319162	12.638323	7.301616e-07		*
PL.1.1	12	9	5.680838	-4.319162	12.638323	7.301616e-07		*

|||||

KP.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2	1589	12	227.030213	NaN	NaN	NaN	*	*	*
MC.24.1	25	36	207.337064	206.174727	-114.349455	8.361236e-13
KS.1.1.2	252	2	198.574836	197.301174	-96.602348	1.169249e-16
XEC.2	921	2	197.286315	201.783492	-105.566985	1.036854e-14
XEC.39	155	2	195.810694	199.541295	-101.082591	1.098314e-15
XEC.9	305	12	193.268152	192.615335	-87.230669	1.079536e-18		*
XEC.8	592	2	193.033005	198.159555	-98.319110	2.763123e-16
KP.3.3	1715	12	192.457197	200.050794	-102.101587	1.829013e-15		*
XEC.32	42	12	192.170275	191.534526	-85.069051	3.666057e-19		*
XEK.5	28	12	191.854108	191.292466	-84.584933	2.869440e-19		*

Target sequence

, 241_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6310_C|T, 6701_C|T, 7528_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13551_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 16887_C|T, 16943_G|T,
17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T,
22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A,
22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C

 Case 55 (XEQ): USA/CO-CDC-QDX33808363/2025



Target: 269 samples       Number of changes: 146                                                   
BC: JN.1 + KP.2           BC BR: 20-21                    BC BR coord: 8866 - 8867          
Direction L1: <<          Initial region span: 1-19,21-146 Gap history (edge excluded): 19-21
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 2.08e-15                                                            
Rec. model vs L1: 1.10e-21 Rec. model vs L2: 3.08e-35                                               
Flags: Model_1BP_Best

JN.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1	17255	19	27.756261	NaN	NaN	NaN	*	*	*
KP.2.2	1334	19	18.419532	8.419532	41.160937	4.088859e-09		*
KP.2.3.10	10	9	17.811654	-33.065210	124.130421	3.934554e-27
PL.1.1	12	9	17.542321	-53.203181	164.406362	7.050252e-36
KP.3.1.2	28	9	16.671559	-2.016098	62.032197	1.201543e-13
JN.1.69	32	9	16.648503	-29.630829	117.261658	1.220948e-25
LF.7.2	35	9	16.500916	-48.563748	155.127496	7.300137e-34
JN.1.50.2	33	9	16.493668	-38.546208	135.092416	1.640445e-29
MK.1	151	9	16.148381	-34.517762	127.035525	9.183263e-28
KP.2.3.7	54	9	16.068823	-44.009436	146.018872	6.942924e-32

|||||

KP.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2	1589	21	207.686381	NaN	NaN	NaN	*	*	*
MC.24.1	25	46	204.783064	177.052837	-86.105674	4.983793e-14
JN.1	17255	1	193.685648	165.951070	-63.902140	7.494105e-19
MR.2	14	46	189.417525	157.189625	-46.379249	1.175710e-22
XEC.2	921	21	187.695236	187.695236	-107.390471	2.081869e-09		*
XEK.5	28	47	186.826807	162.280931	-56.561861	1.909234e-20
XEC.2.2	273	47	185.619187	173.039121	-78.078242	8.992236e-16
XEK.1	88	47	185.381124	161.504865	-55.009729	8.795911e-21
XEC.9	305	47	184.400272	163.854822	-59.709645	9.223014e-20
XEC.2.1	265	47	184.093029	145.075317	-22.150634	6.439060e-28

Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4228_A|T, 4321_C|T, 4901_C|T, 6183_A|G, 6312_C|T, 6651_C|T, 6701_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
8861_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12439_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C,
14396_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 16887_C|T, 16943_G|T, 17410_C|T, 18163_A|G, 18329_C|A, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22149_A|G, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G,
22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T,
25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 55 (XEQ): USA/CT-DPH-1286600001/2025



Target: 269 samples       Number of changes: 138                                                   
BC: KS.1.1.2 + MC.24.1    BC BR: 40-41                    BC BR coord: 17411 - 17412        
Direction L1: <<          Initial region span: 1-34,43-138 Gap history (edge excluded): 34-43
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 2.49e-16                                                            
Rec. model vs L1: 4.77e-36 Rec. model vs L2: 1.53e-36                                               
Flags: Model_1BP_Best

KS.1.1.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KS.1.1.2	252	34	47.019733	NaN	NaN	NaN	*	*	*
KP.3.1.1	12013	27	40.138102	17.412739	65.174522	5.031312e-08
XEC.2	921	24	33.034695	13.813580	72.372840	1.374742e-09
JN.1.13.1	751	27	32.561232	9.482411	81.035178	1.801169e-11
LB.1.3	778	27	32.215153	8.764540	82.470921	8.811178e-12
JN.1	17255	34	31.655936	25.492705	49.014590	1.624728e-04	*	*
JN.1.7	1974	18	30.637924	-1.798158	103.596317	2.273593e-16
JN.1.32	436	18	30.396258	-1.226359	102.452717	4.040472e-16
MC.1.1	107	18	30.184200	-45.383964	190.767928	2.679093e-35
JN.1.8.3	121	27	29.995699	-15.208419	130.416839	3.410545e-22

|||||

MC.24.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.24.1	25	43	181.001520	NaN	NaN	NaN	*	*	*
MC.1	932	49	172.187927	146.537821	-65.075642	1.108975e-11
KP.3.3	1715	43	169.068034	159.832038	-91.664076	6.556852e-06		*
JN.1.4	8971	4	167.852413	142.858196	-57.716391	2.797164e-13
MC.19	221	51	165.658470	133.634976	-39.269952	2.756458e-17
KP.2	1589	43	165.101600	155.866187	-83.732375	1.243706e-07		*
KS.1.1.2	252	2	164.872022	130.085858	-32.171717	7.917827e-19
MC.11	393	49	164.114415	131.015160	-34.030320	2.006780e-18
KP.3	769	49	163.561223	148.132525	-68.265051	5.465393e-11
MC.13	807	49	163.135411	137.454608	-46.909216	1.257061e-15

Target sequence

, 203_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6701_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 9814_T|C,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11124_C|T, 11288_11296, 11727_G|A, 12076_C|T, 12418_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 14773_G|A, 15714_C|T,
15756_T|A, 16887_C|T, 16943_G|T, 17410_C|T, 18163_A|G, 18375_T|C, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C,
22684_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A,
22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T,
26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C,
29734_29759

 Case 55 (XEQ): USA/DC-CDC-2-8398675/2025



Target: 269 samples       Number of changes: 145                                                   
BC: LB.1.3.2 + KP.2       BC BR: 13-14                    BC BR coord: 7118 - 7119          
Direction L1: <<          Initial region span: 1-10,16-145 Gap history (edge excluded): 10-16
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 9.01e-07                                                            
Rec. model vs L1: 4.68e-67 Rec. model vs L2: 1.32e-16                                               
Flags: Model_1BP_Best

LB.1.3.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LB.1.3.2	390	10	20.309495	NaN	NaN	NaN	*	*	*
MC.28	304	10	19.754430	-1.019295	42.038590	5.644495e-08		*
JN.1	17255	12	18.739122	18.543784	2.912431	1.772542e+01	*
LB.1.3	778	10	17.872098	11.441243	17.117514	1.455239e-02	*	*
JN.1.32	436	10	17.755495	11.901429	16.197143	2.305206e-02	*	*
LB.1.7	1971	10	16.294931	3.115380	33.769240	3.527222e-06		*
JN.1.8.3	121	10	14.129862	-2.260347	44.520694	1.633428e-08		*
JN.1.16.3	52	12	13.746642	3.746642	32.506716	6.622749e-06
NY.16	136	10	12.300606	-20.180270	80.360540	2.694901e-16		*
JN.1.4.2	736	10	12.145639	-4.247291	48.494581	2.244013e-09		*

|||||

KP.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2	1589	16	201.442275	NaN	NaN	NaN	*	*	*
KP.3.1.1	12013	3	193.114559	177.728291	-61.456583	2.447752e-02	*
KS.1.1.2	252	16	187.607156	167.607156	-41.214312	9.806992e-07		*
MC.24.1	25	41	186.620020	156.093432	-18.186865	9.835725e-12
KP.3.1	1957	41	184.031878	173.813810	-53.627620	4.880952e-04	*
MC.1	932	46	183.160501	135.289174	23.421652	9.063786e-21
JN.1	17255	1	183.114049	164.570265	-35.140530	4.714679e-08
XEC.2.1	265	41	177.565336	137.332696	19.334608	7.005544e-20
KP.3	769	49	177.548733	144.148001	5.703998	6.384969e-17
XEC.2	921	41	176.312932	155.380305	-16.760610	4.811559e-12

Target sequence

, 241_C|T, 504_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5704_G|T, 6183_A|G, 6701_C|T, 7279_C|T, 7294_G|A, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 14676_C|T, 15714_C|T,
15756_T|A, 16392_T|C, 16887_C|T, 16943_G|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20389_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22323_C|T,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T,
23075_T|C, 23185_C|T, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T,
25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 55 (XEQ): USA/IL-RIPHL_15496_G/2025



Target: 269 samples           Number of changes: 147                                                               
BC: MC.24.1 + LB.1.7 + MC.24.1 BC BR: 3-4, 43-44                    BC BR coord: 896 - 897, 17409 - 17410    
Direction L1: <<              Initial region span: 1-3,17-43,44-147 Gap history (edge excluded): 3-44 -> 3-17
Alt. candidates: [], []                                                                                                   
Model 1BP/2BP comparison:     2BP vs 1BP: 3.13e-28                                                                        
Rec. model vs L1: 5.52e-38    Rec. model vs L2: 2.52e-54                                                           
Flags: Model_2BP_Best

MC.24.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.24.1	25	3	4.677997	None	None	None	*	*	*

|||||

LB.1.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LB.1.7	1971	17	18.791066	NaN	NaN	NaN	*	*	*
JN.1	17255	17	15.216481	-5.280363	122.560725	1.144537e+00	*	*
JN.1.4	8971	17	15.116107	-4.483100	120.966201	2.534509e+00	*	*
KP.2.3	4440	17	10.639991	-11.903808	135.807617	1.518549e-03	*	*
JN.1.1	3081	33	10.526857	-19.939366	151.878733	4.918953e-07
BA.2.86.1	1343	17	7.355318	-18.370930	148.741861	2.364368e-06		*
JN.1.4.5	1757	39	6.345757	-36.794167	185.588335	2.354177e-14
LF.7.6	15	43	5.231571	-94.244932	300.489864	2.640105e-39
JN.1.7.1	120	43	4.761567	-50.407740	212.815479	2.876867e-20
B.1.1.318	1569	43	4.724562	-302.580461	717.160922	8.767591e-130

|||||

MC.24.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.24.1	25	44	184.698786	NaN	NaN	NaN	*	*	*
KP.2	1589	30	181.969180	184.331518	-134.663037	6.441460e-03	*
MR.2	14	44	169.333247	174.052066	-114.104132	2.210228e-07		*
XEC.2	921	44	167.776614	172.458172	-110.916344	4.507221e-08		*
XEC.2.1	265	44	167.475708	172.148486	-110.296971	3.305807e-08		*
KP.3.1	1957	44	167.271401	171.952565	-109.905131	2.720133e-08		*
MC.8.1	174	59	166.171095	143.363447	-52.726894	1.042584e-20
XEK.5	28	44	165.161097	169.805808	-105.611616	3.168524e-09		*
XEC.2.2	273	44	163.953477	168.635326	-103.270653	9.834051e-10		*
XEK.1	88	44	163.715414	168.422805	-102.845610	7.971327e-10		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1738_G|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3787_C|T, 4184_G|A, 4321_C|T, 5300_G|A, 6183_A|G, 6701_C|T, 7331_G|T, 7393_G|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 9693_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11109_C|T, 11288_11296, 11727_G|A, 12418_T|C, 12789_C|T, 12815_C|T, 12827_T|C, 12880_C|T,
13339_T|C, 14265_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 16887_C|T, 16943_G|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22048_T|C, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G,
22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|A, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T,
25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28396_G|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 55 (XEQ): USA/IL-RIPHL_33562_G/2025



Target: 269 samples       Number of changes: 145                                               
BC: XEC.2 + KP.3          BC BR: 136-137                    BC BR coord: 28271 - 28272  
Direction L1: >>          Initial region span: 1-136,137-145 Gap history (edge excluded):
Alt. candidates: [], []                                                                               
Model 1BP/2BP comparison: 1BP vs 2BP: 5.73e-02                                                        
Rec. model vs L1: 8.12e-19 Rec. model vs L2: 1.35e-28                                           
Flags: Model_1BP_Best

XEC.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	136	193.710444	NaN	NaN	NaN	*	*	*
KP.3.1.1	12013	145	189.538884	180.134825	-46.269650	1.271898e-06
KP.2.3	4440	145	187.470520	177.966295	-41.932590	1.452223e-07
JN.1	17255	145	180.465957	171.209609	-28.419219	1.691898e-10
KS.1.1.2	252	111	178.369348	159.505838	-5.011677	1.396231e-15
JN.1.4	8971	145	173.726166	163.385510	-12.771021	6.761139e-14
KP.3.1	1957	145	169.602308	159.056996	-4.113991	8.902761e-16
KP.2	1589	138	159.016689	157.582056	-1.164113	2.036762e-16
KP.3.3	1715	136	153.170217	153.170217	7.659565	2.475721e-18		*
XEC.39	155	110	152.000195	149.885928	14.228144	9.269244e-20

|||||

KP.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3	769	137	15.147852	NaN	NaN	NaN	*	*	*
JN.1.42.1	18	137	13.781451	13.781451	-9.562902	0.254107	*	*
JN.1.51.1	24	137	13.685660	13.685660	-9.371320	0.231078	*	*
JN.1.56	21	137	13.477848	13.477848	-8.955696	0.188247	*	*
MC.36	49	137	13.000573	13.000573	-8.001146	0.116484	*	*
JN.1.27	62	137	12.605402	12.605402	-7.210805	0.078473	*	*
KP.3.4	62	137	12.511552	12.511552	-7.023105	0.071361	*	*
MC.24	831	137	12.244533	12.244533	-6.489066	0.054749	*	*
JN.1.52	150	137	11.735295	11.735295	-5.470591	0.032876	*	*
LB.1.2.2	175	137	11.712458	11.712458	-5.424915	0.032065	*	*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2761_A|C, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4579_T|A, 6183_A|G, 6701_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14262_C|T, 14408_C|T, 15714_C|T,
15756_T|A, 16887_C|T, 16943_G|T, 17410_C|T, 18163_A|G, 18492_A|G, 18804_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22051_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24381_C|T, 24424_A|T, 24469_T|A, 24745_C|T, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26753_C|T, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28311_C|T, 28362_28370, 28705_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 55 (XEQ): USA/MN-MDH-46610/2025



Target: 269 samples        Number of changes: 146                                               
BC: KP.2 + CK.1            BC BR: 142-143                    BC BR coord: 28958 - 28959  
Direction L1: >>           Initial region span: 1-142,143-146 Gap history (edge excluded):
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 7.43e-14 Rec. model vs L2: 0.00e+00                                           
Flags: Model_2BP_Bad_L1_opp

KP.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2	1589	142	200.779066	NaN	NaN	NaN	*	*	*
KP.2.3	4440	146	195.425509	190.516695	-59.033391	3.483110e-05	*
XEC.2	921	136	189.789308	186.155651	-50.311302	4.450853e-07
JN.1	17255	145	180.547259	178.709717	-35.419435	2.600883e-10
JN.1.4	8971	146	177.946561	175.354170	-28.708340	9.079518e-12
KP.3.1.1	12013	145	177.786690	175.585106	-29.170211	1.142748e-11
KP.3.1	1957	145	168.299378	167.601554	-13.203108	3.891429e-15
KS.1.1.2	252	112	166.982337	160.603613	0.792774	3.566311e-18
KP.3	769	142	158.828011	158.828011	4.343977	6.044307e-19		*
KP.3.3	1715	136	156.894467	153.275910	15.448180	2.337979e-21

|||||

CK.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
CK.1	451	143	9.547834	NaN	NaN	NaN	*	*	*
CB.1	82	144	9.064721	-0.935279	11.870559	2.795261e-05	*	*
BA.2.60	31	144	8.948762	-1.051238	12.102477	2.491601e-05	*	*
JN.1.38	247	143	8.096348	8.096348	-6.192696	2.334004e-01	*	*
GR.1	120	144	7.582377	-7.750882	25.501764	3.066941e-08		*
XBB.1.5.80	186	144	7.120634	-2.879366	15.758731	3.996866e-06		*
BQ.1.12	2465	144	6.677357	5.622896	-1.245792	1.974214e-02	*	*
KP.2.3	4440	144	5.298974	4.908814	0.182373	9.657698e-03	*	*
BF.4	1166	144	5.223763	-4.776237	19.552475	6.008022e-07		*
BA.5.3.2	887	144	5.073932	4.348427	1.303147	5.516564e-03	*	*

Target sequence

, 241_C|T, 664_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6701_C|T, 6864_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16887_C|T, 16943_G|T,
17410_C|T, 18163_A|G, 18210_G|T, 18492_A|G, 18648_T|C, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22088_C|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25047_C|T, 25163_C|A, 25207_C|T, 25507_G|A,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29296_C|T, 29510_A|C, 29734_29759, 29807_T|A

 Case 55 (XEQ): USA/NMDOH-2025009737/2025



Target: 269 samples       Number of changes: 143                                                   
BC: JN.1 + MC.24.1        BC BR: 40-41                    BC BR coord: 16949 - 16950        
Direction L1: <<          Initial region span: 1-28,41-143 Gap history (edge excluded): 28-41
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 9.38e-11                                                            
Rec. model vs L1: 5.29e-29 Rec. model vs L2: 4.13e-44                                               
Flags: Model_1BP_Best

JN.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1	17255	28	37.933316	NaN	NaN	NaN	*	*	*
KP.2.3	4440	28	35.954419	29.166822	37.666355	2.773195e+00	*	*
KP.3.1.1	12013	28	32.660241	12.226126	71.547749	1.219079e-07		*
JN.1.4	8971	28	31.196677	24.752323	46.495353	3.354055e-02	*	*
JN.1.48	10	11	24.419246	-26.330485	148.660969	2.196889e-24
MC.13.1	123	12	23.122272	-32.208864	160.417728	6.139833e-27
KP.2.3.11	56	11	22.642094	-43.657710	183.315419	6.538599e-32
JN.1.63	60	11	22.541687	-22.071041	140.142081	1.555617e-22
JN.1.2	650	28	22.494418	-2.361175	100.722350	5.647378e-14		*
JN.1.7	1974	28	22.121485	4.418752	87.162496	4.970080e-11		*

|||||

MC.24.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.24.1	25	41	206.620020	NaN	NaN	NaN	*	*	*
KP.2	1589	19	204.474330	180.618363	-137.236726	5.109089e-12
MR.2	14	41	191.254480	186.756808	-149.513615	2.359066e-09		*
XEC.2	921	31	189.460717	184.793250	-145.586500	3.322943e-10
XEK.5	28	41	187.082331	187.082331	-150.164662	3.265020e-09		*
KP.3.1	1957	41	186.650574	182.163690	-140.327380	2.395126e-11		*
XEC.2.2	273	41	185.874711	185.874711	-147.749421	9.785003e-10		*
XEK.1	88	41	185.636648	185.636648	-147.273297	7.697156e-10		*
XEC.9	305	41	184.655796	184.655796	-145.311592	2.888828e-10		*
KP.2.3	4440	1	184.545901	155.379078	-86.758157	5.581498e-23

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1601_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6285_C|T, 6701_C|T, 7564_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 8947_C|T, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12685_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15720_C|T, 15756_T|A, 16887_C|T, 16943_G|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G,
22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A,
23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24090_A|G, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 55 (XEQ): USA/NMDOH-2025013200/2025



Target: 269 samples        Number of changes: 139                                             
BC: JN.9 + KP.2            BC BR: 11-12                    BC BR coord: 7118 - 7119    
Direction L1: <<           Initial region span: 1-11,12-139 Gap history (edge excluded):
Alt. candidates: [], []                                                                              
Model 1BP/2BP comparison:  1BP vs 2BP: 4.90e-02                                                      
Rec. model vs L1: 5.28e-125 Rec. model vs L2: 2.54e-32                                         
Flags: Model_1BP_Best

JN.9 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.9	55	11	20.431130	NaN	NaN	NaN	*	*	*
JN.11	67	10	15.851612	5.851612	22.296776	4.655716e-07		*
JN.18	316	11	15.144993	15.144993	3.710015	5.067032e-03	*	*
JN.3	321	10	14.930933	-1.375664	36.751328	3.390071e-10		*
BA.2.86.1	1343	10	14.446675	4.446675	25.106651	1.142359e-07		*
MC.10.2.1	11	10	13.901608	-10.526839	55.053679	3.600927e-14		*
KP.2.3.13	25	10	13.869085	-0.517726	35.035452	7.971327e-10		*
JN.7	82	9	13.649232	-5.489980	44.979961	5.534610e-12
NL.19	18	10	13.447284	3.447284	27.105433	4.202505e-08		*
JN.1.7	1974	11	13.362795	13.362795	7.274410	8.544949e-04	*	*

|||||

KP.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2	1589	12	221.528527	NaN	NaN	NaN	*	*	*
XEC.2	921	1	198.733225	194.559029	-99.118058	1.936769e-12
KS.1.1.2	252	5	192.161982	178.803010	-67.606019	2.784635e-19
KP.3.3	1715	12	192.053222	192.053222	-94.106443	1.581868e-13		*
XEC.9	305	14	191.094001	184.696944	-79.393888	1.006382e-16
XEC.8	592	5	187.116748	180.098728	-70.197457	1.016669e-18
XEC.32	42	5	181.881976	172.252609	-54.505217	3.982350e-22
MC.24.1	25	14	181.358888	174.961831	-59.923662	5.955332e-21
KP.3.1.1	12013	1	180.974185	174.257093	-58.514186	2.942581e-21
KP.3	769	14	178.792602	172.394244	-54.788488	4.580793e-22

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1684_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 6183_A|G, 6701_C|T, 7842_A|G, 7945_C|T, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16887_C|T, 16943_G|T, 17410_C|T,
18163_A|G, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25003_A|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C,
29700_A|G, 29734_29759

 Case 55 (XEQ): USA/NMDOH-2025014470/2025



Target: 269 samples        Number of changes: 142                                             
BC: JN.9 + KP.2            BC BR: 12-13                    BC BR coord: 7118 - 7119    
Direction L1: <<           Initial region span: 1-12,13-142 Gap history (edge excluded):
Alt. candidates: [], []                                                                              
Model 1BP/2BP comparison:  1BP vs 2BP: 2.54e-03                                                      
Rec. model vs L1: 1.32e-124 Rec. model vs L2: 1.32e-33                                         
Flags: Model_1BP_Best

JN.9 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.9	55	12	21.906785	NaN	NaN	NaN	*	*	*
JN.11	67	11	18.228521	8.228521	17.542959	1.150861e-06		*
NL.19	18	11	17.426195	7.426195	19.147610	5.145362e-07		*
JN.18	316	12	16.818149	16.818149	0.363701	6.188887e-03	*	*
JN.3	321	11	15.047946	-1.258651	36.517302	8.700983e-11		*
BA.2.86.1	1343	11	14.806444	4.806444	24.387112	3.745971e-08		*
LB.1.3.1	292	11	14.425151	4.425151	25.149698	2.561725e-08		*
JN.7	82	10	14.032355	-5.106858	44.213716	1.860827e-12
JN.1.7	1974	12	13.049726	13.049726	7.900548	1.426666e-04	*	*
MC.24	831	12	12.672824	8.286013	17.427974	1.215932e-06		*

|||||

KP.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2	1589	13	201.681620	NaN	NaN	NaN	*	*	*
KP.3.1.1	12013	3	190.932653	184.219710	-74.439421	2.613475e-08
JN.1	17255	1	181.936012	171.807102	-49.614203	1.060358e-13
KP.2.3	4440	3	174.405635	168.623435	-43.246870	4.409567e-15
MC.24.1	25	41	173.651463	154.961831	-15.923662	5.125802e-21
JN.1.4	8971	4	170.381607	164.594122	-35.188244	7.837709e-17
XEC.2	921	1	170.178188	165.842387	-37.684774	2.721985e-16
XEC.2.2	273	42	169.780712	153.296698	-12.593396	9.697538e-22
XEC.9	305	42	168.325918	156.821064	-19.642127	3.292680e-20
XEK.1	88	42	164.814103	149.955450	-5.910899	3.436512e-23

Target sequence

, 241_C|T, 509_523, 670_T|G, 897_C|A, 1684_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 6183_A|G, 6701_C|T, 7842_A|G, 7945_C|T, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10125_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16887_C|T,
16943_G|T, 17410_C|T, 18163_A|G, 18167_C|T, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24292_A|G, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27527_C|T, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T,
28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 55 (XEQ): USA/NY-USAFSAM-S23702/2025



Target: 269 samples        Number of changes: 144                                                       
BC: KP.2 + JN.1.52         BC BR: 136-137                    BC BR coord: 28361 - 28362          
Direction L1: >>           Initial region span: 1-136,138-144 Gap history (edge excluded): 136-138
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 4.01e-07 Rec. model vs L2: 5.24e-64                                                   
Flags: Model_2BP_Bad_L1_opp

KP.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2	1589	136	204.827501	NaN	NaN	NaN	*	*	*
XEC.2	921	134	190.823447	186.492555	-60.985111	1.089458e-08
KS.1.1.2	252	136	185.749577	185.749577	-59.499153	5.172033e-09		*
XEC.8	592	134	181.561572	177.242591	-42.485182	1.047097e-12
KP.2.3	4440	144	177.462439	169.659460	-27.318919	5.319405e-16
XEC.18	165	134	172.919344	168.613832	-25.227664	1.870791e-16
KP.3.3	1715	134	172.642419	168.324704	-24.649408	1.399845e-16
KP.3.1.1	12013	136	169.006037	169.006037	-26.012074	2.763123e-16		*
JN.1	17255	141	167.703313	163.908312	-15.816624	1.693050e-18
XEC.39	155	134	167.689853	163.383549	-14.767098	1.001533e-18

|||||

JN.1.52 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.52	150	138	12.208037	NaN	NaN	NaN	*	*	*
JN.1.4.3	129	138	11.562933	1.562933	16.874135	5.246625e-01	*	*
MC.10.1	650	138	10.021102	-7.652555	35.305110	5.196189e-05	*	*
MC.13	807	138	9.910126	-0.089874	20.179749	1.002588e-01	*	*
KP.3.1	1957	138	8.940001	-1.059999	22.119999	3.800643e-02	*	*
KP.2.3	4440	138	8.828691	7.802979	4.394041	2.690777e+02	*	*
KP.3.1.1	12013	138	7.885735	-2.114265	24.228530	1.323355e-02	*	*
JN.1.4	8971	138	7.454435	5.032233	9.935534	1.677685e+01	*	*
BQ.1.1.1	1179	142	7.119877	-14.746907	49.493813	4.330490e-08
BN.1.3	1498	142	6.425820	-11.991691	43.983383	6.807981e-07

Target sequence

, 241_C|T, 509_523, 575_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6701_C|T, 7528_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 9655_T|C, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11020_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15720_C|T, 15756_T|A, 16887_C|T, 16943_G|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26606_C|T, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28690_G|T,
28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29335_T|C, 29510_A|C, 29734_29759

 Case 58 (XFG): BHR/25020274266/2025



Target: 530 samples         Number of changes: 152                                                                          
BC: XFG.3 + FY.1.4.1 + XFG.3 BC BR: 131-132, 136-137                   BC BR coord: 26872 - 26873, 27387 - 27388      
Direction L1: >>            Initial region span: 1-131,132-136,138-152 Gap history (edge excluded): 131-138 -> 136-138
Alt. candidates: [], []                                                                                                            
Model 1BP/2BP comparison:   2BP vs 1BP: 2.97e-01                                                                                   
Rec. model vs L1: 2.86e-08  Rec. model vs L2: 0.00e+00                                                                      
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	131	290.226493	NaN	NaN	NaN	*	*	*
LF.7	58	131	289.964059	281.681666	-227.363333	7.171897e-02	*	*
XFG.2	500	131	273.151789	267.357038	-198.714076	4.308892e-08		*
XFG.3.1	87	131	268.035180	261.461788	-186.923576	1.186314e-10		*
XFG.1	14	131	252.185044	246.515339	-157.030678	3.834145e-17		*
LF.7.7.1	188	131	220.837599	205.793623	-75.587245	7.928614e-35		*
LF.7.6	15	131	210.184030	188.345024	-40.690048	2.092949e-42		*
LF.7.3	54	143	208.760913	190.967197	-45.934395	2.874816e-41
LF.7.1.8	44	131	206.589098	184.696931	-33.393863	5.439810e-44		*
LF.7.1	165	131	203.280392	193.079604	-50.159207	2.383104e-40		*

|||||

FY.1.4.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
FY.1.4.1	41	136	13.108949	NaN	NaN	NaN	*	*	*
GS.7	16	136	11.905952	11.905952	-13.811904	0.299692	*	*
JY.1.1	42	136	11.005410	11.005410	-12.010820	0.121846	*	*
XBB.1.22	77	136	10.399274	10.399274	-10.798548	0.066537	*	*
BA.2.32	367	136	9.922672	9.922672	-9.845345	0.041378	*	*
GV.1	137	136	9.823099	9.823099	-9.646197	0.037441	*	*
XBB.1.5.46	613	136	9.547214	9.547214	-9.094428	0.028297	*	*
XBB.1.16.15	1675	137	9.529018	8.412148	-6.824296	0.009095	*	*
XBB.1.5.10	817	137	9.164369	8.022716	-6.045433	0.006189	*	*
LP.8.1	1124	137	8.534839	7.712197	-5.424393	0.004517	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	138	4.08917	None	None	None	*	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 5911_T|C, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 14747_A|G,
15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18326_C|T, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T,
25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27209_A|G, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28475_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29671_A|G, 29734_29759

 Case 58 (XFG): BHR/25100010185/2025



Target: 530 samples        Number of changes: 153                                                       
BC: XFG.3 + PR.2           BC BR: 150-151                    BC BR coord: 29412 - 29413          
Direction L1: >>           Initial region span: 1-143,151-153 Gap history (edge excluded): 143-151
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 1.54e-08 Rec. model vs L2: 4.65e-186                                                  
Flags: Model_2BP_Bad_L1_opp

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	143	286.186454	NaN	NaN	NaN	*	*	*
LF.7	58	143	285.971646	274.809638	-203.619276	6.959935e-02	*	*
XFG.2	500	143	279.652152	265.062027	-184.124054	4.057271e-06		*
XFG.3.1	87	143	275.423658	266.712656	-187.425311	2.123202e-05	*	*
XFG.1	14	143	248.245114	239.534111	-133.068223	3.333246e-17		*
LF.7.6	15	143	206.244100	174.700261	-3.400522	2.319448e-45		*
LF.7.7.1	188	143	204.706097	190.758652	-35.517305	2.188538e-38		*
LF.7.1.8	44	143	202.626179	177.888976	-9.777951	5.633574e-44		*
LF.7.1	165	143	199.315922	186.173883	-26.347767	2.233129e-40		*
LF.7.3	54	143	196.001218	171.264015	3.471970	7.474516e-47		*

|||||

PR.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
PR.2	20	151	10.538285	NaN	NaN	NaN	*	*	*
EF.2	344	150	10.174713	8.379717	-10.759434	0.115325	*	*
NY.6	30	151	9.535464	9.535464	-13.070928	0.366045	*	*
LP.8.1.1	2345	151	8.446588	8.446588	-10.893177	0.123070	*	*
EG.10.1	101	151	7.656183	7.656183	-9.312367	0.055855	*	*
NY.13	463	150	7.250896	5.282981	-4.565963	0.005221	*	*
XBB.1.5.30	317	151	5.902512	5.902512	-5.805024	0.009706	*	*
LP.8.1	1124	150	5.776128	4.471992	-2.943983	0.002311	*	*
BF.7.4	1716	151	5.002369	5.002369	-4.004739	0.003927	*	*
MC.13	807	150	4.921771	4.895747	-3.791494	0.003535	*	*

Target sequence

, 106_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 5911_T|C, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12885_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 14747_A|G, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G,
22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27209_A|G, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28475_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29194_T|A, 29409_C|T, 29510_A|C, 29671_A|G, 29734_29759

 Case 58 (XFG): BHR/25100013134/2025



Target: 530 samples        Number of changes: 156                                                       
BC: LF.7 + PR.2            BC BR: 153-154                    BC BR coord: 29412 - 29413          
Direction L1: >>           Initial region span: 1-134,154-156 Gap history (edge excluded): 134-154
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 1.60e-08 Rec. model vs L2: 7.59e-229                                                  
Flags: Model_2BP_Bad_L1_opp

LF.7 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	134	273.955316	NaN	NaN	NaN	*	*	*
XFG.3	480	134	260.226493	247.475452	-142.950903	1.206744e-05	*	*
XFG.2	500	134	255.682029	237.143963	-122.287925	3.938701e-10		*
XFG.3.1	87	134	238.035180	225.208799	-98.417597	2.582548e-15		*
XFG.1	14	134	222.185044	209.534111	-67.068223	4.022373e-22		*
LF.7.7.1	188	134	204.751470	186.864095	-21.728191	5.741514e-32		*
LF.7.6	15	134	180.184030	144.700261	62.599478	2.798979e-50		*
LF.7.3	54	146	178.760913	154.023710	43.952580	3.139031e-46
LF.7.1.8	44	134	176.589098	147.888976	56.222049	6.798279e-49		*
LF.7.1	165	134	173.280392	156.173883	39.652233	2.694814e-45		*

|||||

PR.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
PR.2	20	154	10.538285	NaN	NaN	NaN	*	*	*
EF.2	344	153	10.174713	8.379717	-10.759434	0.115325	*	*
NY.6	30	154	9.535464	9.535464	-13.070928	0.366045	*	*
LP.8.1.1	2345	154	8.446588	8.446588	-10.893177	0.123070	*	*
EG.10.1	101	154	7.656183	7.656183	-9.312367	0.055855	*	*
NY.13	463	153	7.250896	5.282981	-4.565963	0.005221	*	*
XBB.1.5.30	317	154	5.902512	5.902512	-5.805024	0.009706	*	*
LP.8.1	1124	153	5.776128	4.471992	-2.943983	0.002311	*	*
BF.7.4	1716	154	5.002369	5.002369	-4.004739	0.003927	*	*
MC.13	807	153	4.921771	4.895747	-3.791494	0.003535	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2676_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4230_C|T, 4321_C|T, 5239_C|T, 5911_T|C, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 14747_A|G, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 17637_A|G, 18163_A|G, 18326_C|T, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27209_A|G, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28475_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 28988_28993, 29409_C|T,
29510_A|C, 29671_A|G, 29734_29759

 Case 58 (XFG): BHR/25020274266/2025



Target: 530 samples         Number of changes: 152                                                                          
BC: XFG.3 + FY.1.4.1 + XFG.3 BC BR: 131-132, 136-137                   BC BR coord: 26872 - 26873, 27387 - 27388      
Direction L1: >>            Initial region span: 1-131,132-136,138-152 Gap history (edge excluded): 131-138 -> 136-138
Alt. candidates: [], []                                                                                                            
Model 1BP/2BP comparison:   2BP vs 1BP: 2.97e-01                                                                                   
Rec. model vs L1: 2.86e-08  Rec. model vs L2: 0.00e+00                                                                      
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	131	290.226493	NaN	NaN	NaN	*	*	*
LF.7	58	131	289.964059	281.681666	-227.363333	7.171897e-02	*	*
XFG.2	500	131	273.151789	267.357038	-198.714076	4.308892e-08		*
XFG.3.1	87	131	268.035180	261.461788	-186.923576	1.186314e-10		*
XFG.1	14	131	252.185044	246.515339	-157.030678	3.834145e-17		*
LF.7.7.1	188	131	220.837599	205.793623	-75.587245	7.928614e-35		*
LF.7.6	15	131	210.184030	188.345024	-40.690048	2.092949e-42		*
LF.7.3	54	143	208.760913	190.967197	-45.934395	2.874816e-41
LF.7.1.8	44	131	206.589098	184.696931	-33.393863	5.439810e-44		*
LF.7.1	165	131	203.280392	193.079604	-50.159207	2.383104e-40		*

|||||

FY.1.4.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
FY.1.4.1	41	136	13.108949	NaN	NaN	NaN	*	*	*
GS.7	16	136	11.905952	11.905952	-13.811904	0.299692	*	*
JY.1.1	42	136	11.005410	11.005410	-12.010820	0.121846	*	*
XBB.1.22	77	136	10.399274	10.399274	-10.798548	0.066537	*	*
BA.2.32	367	136	9.922672	9.922672	-9.845345	0.041378	*	*
GV.1	137	136	9.823099	9.823099	-9.646197	0.037441	*	*
XBB.1.5.46	613	136	9.547214	9.547214	-9.094428	0.028297	*	*
XBB.1.16.15	1675	137	9.529018	8.412148	-6.824296	0.009095	*	*
XBB.1.5.10	817	137	9.164369	8.022716	-6.045433	0.006189	*	*
LP.8.1	1124	137	8.534839	7.712197	-5.424393	0.004517	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	138	4.08917	None	None	None	*	*	*

Target sequence

 Case 58 (XFG): BHR/25280014848/2025



Target: 530 samples        Number of changes: 153                                                       
BC: LF.7 + LP.8.1.1        BC BR: 142-143                    BC BR coord: 28311 - 28312          
Direction L1: >>           Initial region span: 1-142,146-153 Gap history (edge excluded): 142-146
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 1.27e-05 Rec. model vs L2: 4.91e-171                                                  
Flags: Model_2BP_Bad_L1_opp

LF.7 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	142	301.218402	NaN	NaN	NaN	*	*	*
XFG.3	480	142	294.117659	294.117659	-264.235319	8.251049e-04	*	*
XFG.2	500	144	269.959325	268.429152	-212.858304	5.747566e-15
XFG.3.1	87	142	263.316547	263.316547	-202.633093	3.451975e-17		*
XFG.1	14	142	247.466411	247.466411	-170.932822	4.513362e-24		*
LF.7.7.1	188	142	213.480793	213.480793	-102.961587	7.852395e-39		*
LF.7.1.4	12	142	206.562754	206.562754	-89.125508	7.795713e-42		*
LF.7.6	15	142	205.465397	205.465397	-86.930793	2.594967e-42		*
LF.7.1.8	44	142	201.847475	201.847475	-79.694950	6.950017e-44		*
LF.7.1	165	144	201.180062	198.561759	-73.123519	2.602127e-45

|||||

LP.8.1.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LP.8.1.1	2345	146	12.668692	NaN	NaN	NaN	*	*	*
NY.13	463	146	12.513693	-6.716280	41.432561	8.607080e-01	*	*
LP.8.1	1124	146	11.038925	-8.198516	44.397031	1.949524e-01	*	*
PR.2	20	151	10.538285	-13.420215	54.840429	1.054172e-03	*
MC.13	807	146	10.184567	-9.052969	46.105939	8.290997e-02	*	*
EF.2	344	150	10.174713	-24.572325	77.144651	1.515402e-08
NY.6	30	151	9.535464	-14.423036	56.846072	3.858739e-04	*
EG.10.1	101	151	7.656183	-37.296826	102.593651	4.509523e-14
KP.3.1.1	12013	146	6.638411	-12.606640	53.213280	2.381559e-03	*	*
XBB.1.5.30	317	151	5.902512	-31.680096	91.360192	1.237924e-11

Target sequence

, 241_C|T, 509_523, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 5911_T|C, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
14747_A|G, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23148_A|G, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27209_A|G, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28313_C|T, 28362_28370, 28475_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29671_A|G, 29734_29759

 Case 58 (XFG): BHR/25280016045/2025



Target: 530 samples        Number of changes: 156                                                       
BC: LF.7 + PR.2            BC BR: 153-154                    BC BR coord: 29412 - 29413          
Direction L1: >>           Initial region span: 1-133,154-156 Gap history (edge excluded): 133-154
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 1.60e-08 Rec. model vs L2: 7.59e-229                                                  
Flags: Model_2BP_Bad_L1_opp

LF.7 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	133	283.955316	NaN	NaN	NaN	*	*	*
XFG.3	480	133	270.226493	247.475452	-142.950903	1.206744e-05	*	*
XFG.2	500	133	265.682029	237.143963	-122.287925	3.938701e-10		*
XFG.3.1	87	133	248.035180	225.208799	-98.417597	2.582548e-15		*
XFG.1	14	133	232.185044	209.534111	-67.068223	4.022373e-22		*
LF.7.7.1	188	133	214.751470	186.864095	-21.728191	5.741514e-32		*
LF.7.6	15	133	190.184030	161.171016	29.657969	3.979511e-43		*
LF.7.3	54	145	188.760913	154.023710	43.952580	3.139031e-46
LF.7.1.8	44	133	186.589098	147.888976	56.222049	6.798279e-49		*
LF.7.1	165	133	183.280392	156.173883	39.652233	2.694814e-45		*

|||||

PR.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
PR.2	20	154	10.538285	NaN	NaN	NaN	*	*	*
EF.2	344	153	10.174713	8.379717	-10.759434	0.115325	*	*
NY.6	30	154	9.535464	9.535464	-13.070928	0.366045	*	*
LP.8.1.1	2345	154	8.446588	8.446588	-10.893177	0.123070	*	*
EG.10.1	101	154	7.656183	7.656183	-9.312367	0.055855	*	*
NY.13	463	153	7.250896	5.282981	-4.565963	0.005221	*	*
XBB.1.5.30	317	154	5.902512	5.902512	-5.805024	0.009706	*	*
LP.8.1	1124	153	5.776128	4.471992	-2.943983	0.002311	*	*
BF.7.4	1716	154	5.002369	5.002369	-4.004739	0.003927	*	*
MC.13	807	153	4.921771	4.895747	-3.791494	0.003535	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2676_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 5911_T|C, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
14747_A|G, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 17637_A|G, 18163_A|G, 18326_C|T, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27209_A|G, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28475_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 28988_28993, 29041_G|A, 29409_C|T,
29510_A|C, 29671_A|G, 29734_29759

 Case 58 (XFG): BHR/25280016706/2025



Target: 530 samples        Number of changes: 151                                           
BC: JN.1.8.1 + LF.7        BC BR: 5-6                    BC BR coord: 941 - 942      
Direction L1: <<           Initial region span: 1-5,6-151 Gap history (edge excluded):
Alt. candidates: [], []                                                                            
Model 1BP/2BP comparison:  -                                                                       
Rec. model vs L1: 3.97e-131 Rec. model vs L2: 1.42e-14                                       
Flags: Model_2BP_Bad_L1_opp

JN.1.8.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.8.1	1498	5	8.870164	NaN	NaN	NaN	*	*	*
JN.1.8.2	17	4	8.566187	-1.433813	12.867625	0.000033	*	*
JN.2.3	36	4	8.407135	-1.592865	13.185731	0.000029	*	*
MC.28.1	17	4	7.771146	-2.228854	14.457708	0.000015	*	*
JN.3	321	4	7.761717	-2.238283	14.476565	0.000015	*	*
JN.1.8	352	4	7.726793	-2.273207	14.546415	0.000014	*	*
LZ.2.1	10	4	7.608627	-2.391373	14.782746	0.000013	*	*
MC.17.1	10	4	7.608627	-2.391373	14.782746	0.000013	*	*
JN.1.28.1	11	4	7.513317	-2.486683	14.973366	0.000012	*	*
LD.1.1	11	4	7.513317	-2.486683	14.973366	0.000012	*	*

|||||

LF.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	6	315.993193	NaN	NaN	NaN	*	*	*
XFG.3	480	6	315.966793	315.966793	-293.933586	9.704455e-01	*	*
XFG.2	500	6	311.198751	303.660121	-269.320242	4.395189e-06		*
XFG.3.1	87	6	282.157898	282.157898	-226.315796	2.021372e-15		*
XFG.1	14	6	267.211449	267.211449	-196.422899	6.500454e-22		*
LF.7.1.8	44	16	236.949787	231.441999	-124.883998	1.897711e-37
LF.7.1	165	28	234.778805	224.430262	-110.860524	1.713270e-40
LF.7.7.1	188	31	224.840478	206.726282	-75.452563	3.504628e-48
LF.7.6	15	3	212.619381	202.234498	-66.468997	3.932419e-50
LF.7.1.2	26	28	206.014702	195.612183	-53.224366	5.217456e-53

Target sequence

, 241_C|T, 510_518, 670_T|G, 897_C|A, 936_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7164_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9079_A|G, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10039_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): OZ263366



Target: 530 samples        Number of changes: 155                                               
BC: NM.2 + XFG.3           BC BR: 6-7                    BC BR coord: 3037 - 3038        
Direction L1: <<           Initial region span: 1-6,8-155 Gap history (edge excluded): 6-8
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 2.16e-252 Rec. model vs L2: 5.69e-09                                           
Flags: Model_2BP_Bad_L1_opp

NM.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
NM.2	28	6	11.733311	NaN	NaN	NaN	*	*	*
LP.7	57	6	11.559075	11.559075	-9.118150	0.839457	*	*
KP.2.24	44	6	10.665037	10.665037	-7.330075	0.343009	*	*
MC.14	35	6	10.458940	10.458940	-6.917881	0.279431	*	*
KP.2.3.13	25	6	9.649415	9.649415	-5.298830	0.124307	*	*
KP.3.4	62	6	9.012578	9.012578	-4.025156	0.065875	*	*
JN.1.69	32	6	8.997090	8.997090	-3.994179	0.064570	*	*
JN.1.18.5	37	6	8.851908	8.851908	-3.703815	0.055855	*	*
JN.1.1.6	13	4	8.123635	1.960207	10.079587	0.000057	*
KP.2.11	40	6	8.080799	8.080799	-2.161598	0.025861	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	8	285.679194	NaN	NaN	NaN	*	*	*
XFG.2	500	8	256.490665	246.490665	-142.981330	2.103508e-13		*
LF.7	58	8	250.998680	240.998680	-131.997360	8.682951e-16		*
XFG.3.1	87	8	218.998816	208.998816	-67.997631	1.099623e-29		*
XFG.1	14	8	201.981146	191.981146	-33.962292	4.462229e-37		*
LF.7.1	165	21	192.943420	169.563639	10.872723	8.219418e-47
LF.7.7.1	188	35	168.118663	136.953669	76.092663	5.655851e-61
LF.7.1.8	44	21	165.926387	142.524551	64.950898	1.484288e-58
LF.7.7.2	239	21	155.215357	122.565540	104.868919	3.184200e-67
LF.7.3	54	21	154.493004	136.742675	76.514650	4.584544e-61

Target sequence

, 106_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3172_T|C, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 5581_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8278_T|C, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12534_C|T, 12788_A|G, 12789_C|T, 12815_C|T,
12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 14568_T|A, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19518_G|T, 19955_C|T, 20055_A|G, 20178_C|T,
21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21762_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A,
22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26769_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 27923_C|T, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C,
28958_C|A, 29409_C|T, 29510_A|C

 Case 58 (XFG): OZ263370



Target: 530 samples         Number of changes: 150                                                             
BC: XFG.3 + LU.2.1.1 + XFG.3 BC BR: 7-8, 9-10                   BC BR coord: 3566 - 3567, 4188 - 4189    
Direction L1: <<            Initial region span: 1-7,8-9,11-150 Gap history (edge excluded): 7-11 -> 9-11
Alt. candidates: [], []                                                                                               
Model 1BP/2BP comparison:   2BP vs 1BP: 8.67e-02                                                                      
Rec. model vs L1: 2.74e-07  Rec. model vs L2: 6.37e-221                                                        
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	7	12.929009	None	None	None	*	*	*

|||||

LU.2.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LU.2.1.1	49	9	7.467971	NaN	NaN	NaN	*	*	*
MC.36	49	9	7.467971	7.467971	-10.935941	1.000000	*	*
XBB.1.5.86	101	9	6.744670	6.744670	-9.489341	0.484325	*	*
FL.13	151	9	6.342511	6.342511	-8.685022	0.324652	*	*
XBB.2.3	695	9	6.202173	6.202173	-8.404347	0.280832	*	*
BA.1.21.1	65	8	6.108827	-3.891173	11.782347	0.000012	*	*
BA.5.1.2	2225	9	4.344527	4.344527	-4.689053	0.043937	*	*
B.1.1.25	541	8	3.989795	-6.010205	16.020411	0.000001		*
EG.5.1.4	1717	9	3.911457	3.911457	-3.822914	0.028439	*	*
BA.5.2	49968	9	3.872117	3.872117	-3.744233	0.027324	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	11	316.228088	NaN	NaN	NaN	*	*	*
LF.7	58	11	304.248505	307.214112	-274.428224	6.524149e-06		*
XFG.2	500	11	299.421298	302.413148	-264.826297	5.369210e-08		*
XFG.3.1	87	11	272.334253	275.208518	-210.417036	8.221082e-20		*
XFG.1	14	11	255.177861	258.213970	-176.427940	3.420537e-27		*
LF.7.1	165	12	222.566038	215.553253	-91.106506	1.016463e-45		*
LF.7.7.1	188	12	218.986556	211.957879	-83.915759	2.791277e-47		*
LF.7.1.8	44	12	215.721266	208.687865	-77.375731	1.060865e-48		*
LF.7.6	15	12	200.487112	193.523220	-47.046441	2.751593e-55		*
LF.7.3	54	12	197.040048	190.000306	-40.000612	8.103939e-57		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3754_A|G, 4184_G|A, 4206_C|T, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16394_C|T, 16600_T|C, 17410_C|T, 17825_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28805_G|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

 Case 58 (XFG): OZ263399



Target: 530 samples        Number of changes: 151                                                               
BC: XFG.3 + XBB.2.3 + XFG.3 BC BR: 7-8, 10-11                   BC BR coord: 3566 - 3567, 4205 - 4206     
Direction L1: <<           Initial region span: 1-7,8-10,12-151 Gap history (edge excluded): 7-12 -> 10-12
Alt. candidates: [], []                                                                                                
Model 1BP/2BP comparison:  2BP vs 1BP: 5.48e-08                                                                        
Rec. model vs L1: 4.63e-13 Rec. model vs L2: 0.00e+00                                                           
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	7	12.929009	None	None	None	*	*	*

|||||

XBB.2.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XBB.2.3	695	10	10.740845	NaN	NaN	NaN	*	*	*
LU.2.1.1	49	9	7.467971	-2.532029	11.064059	1.725489e-06		*
MC.36	49	9	7.467971	-2.532029	11.064059	1.725489e-06		*
XBB.1.5.86	101	9	6.744670	-3.255330	12.510659	8.356968e-07		*
FL.13	151	9	6.342511	-3.657489	13.314978	5.601843e-07		*
BA.1.21.1	65	8	6.108827	-13.891173	33.782347	2.010606e-11
BA.5.1.2	2225	9	4.344527	-5.655473	17.310947	7.581270e-08		*
B.1.1.25	541	8	3.989795	-16.010205	38.020411	2.413363e-12
EG.5.1.4	1717	9	3.911457	-6.088543	18.177086	4.907088e-08		*
BA.5.2	49968	9	3.872117	-6.127883	18.255767	4.714679e-08		*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	12	316.228088	NaN	NaN	NaN	*	*	*
LF.7	58	12	304.248505	307.214112	-274.428224	6.524149e-06		*
XFG.2	500	12	299.421298	302.413148	-264.826297	5.369210e-08		*
XFG.3.1	87	12	272.334253	275.208518	-210.417036	8.221082e-20		*
XFG.1	14	12	255.177861	258.213970	-176.427940	3.420537e-27		*
LF.7.1	165	13	222.566038	215.553253	-91.106506	1.016463e-45		*
LF.7.7.1	188	13	218.986556	211.957879	-83.915759	2.791277e-47		*
LF.7.1.8	44	13	215.721266	208.687865	-77.375731	1.060865e-48		*
LF.7.6	15	13	200.487112	193.523220	-47.046441	2.751593e-55		*
LF.7.3	54	13	197.040048	190.000306	-40.000612	8.103939e-57		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3754_A|G, 4184_G|A, 4205_G|T, 4206_C|T, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16394_C|T, 16600_T|C, 17410_C|T, 17825_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28805_G|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

 Case 58 (XFG): OZ271485



Target: 530 samples             Number of changes: 136                                                                  
BC: XFG.3.1 + LF.7.7.1 + XFG.3.1 BC BR: 10-11, 14-15                   BC BR coord: 4330 - 4331, 7841 - 7842      
Direction L1: <<                Initial region span: 1-10,12-14,15-136 Gap history (edge excluded): 10-15 -> 10-12
Alt. candidates: [], []                                                                                                        
Model 1BP/2BP comparison:       2BP vs 1BP: 5.25e-03                                                                           
Rec. model vs L1: 2.18e-15      Rec. model vs L2: 2.10e-60                                                              
Flags: Model_2BP_Best

XFG.3.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3.1	87	10	5.990321	None	None	None	*	*	*

|||||

LF.7.7.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7.7.1	188	12	15.074492	NaN	NaN	NaN	*	*	*
JN.1.41	121	13	9.369512	-10.630488	43.260977	1.511490e-07		*
B.1.587	60	14	6.461167	-42.454172	106.908344	2.280254e-21
BA.1.13	393	14	4.581702	-29.556660	81.113320	9.128136e-16
A.2.5	513	14	4.315235	-48.475964	118.951927	5.540264e-24
P.2	983	14	3.664902	-9.262281	40.524562	5.948242e-07
BE.1.4	990	14	3.657806	-26.342194	74.684388	2.273206e-14
B.1.595	1332	14	3.361074	-26.638926	75.277851	1.684033e-14
BA.5.1.22	4997	14	3.137530	-12.348473	46.696947	2.706566e-08
BQ.1.14	1843	14	3.036361	-26.963639	75.927278	1.216760e-14

|||||

XFG.3.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3.1	87	15	261.526954	NaN	NaN	NaN	*	*	*
XFG.3	480	5	249.636789	254.612995	-183.225991	2.498050e-06
LF.7	58	15	245.337818	249.087481	-172.174961	9.907240e-09		*
XFG.2	500	15	237.198082	242.988315	-159.976631	2.233201e-11		*
XFG.1	14	15	214.250354	220.078832	-114.157664	2.507502e-21		*
LF.7.7.1	188	12	188.225685	160.951726	4.096548	5.240932e-47
LF.7.3.1	26	15	178.158771	166.018755	-6.037510	8.342218e-45		*
LF.7.1	165	15	177.393614	165.241403	-4.482806	3.824123e-45		*
LF.7.1.8	44	15	168.438655	156.229129	13.541741	4.672385e-49		*
LF.7.9	20	15	164.433830	152.399175	21.201650	1.014357e-50		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1784_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4214_T|C, 4321_C|T, 4354_G|A, 5239_C|T, 6183_A|G, 6643_T|C, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T,
22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28372_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): OZ272392



Target: 530 samples         Number of changes: 149                                                             
BC: XFG.3 + LU.2.1.1 + XFG.3 BC BR: 7-8, 9-10                   BC BR coord: 3566 - 3567, 4188 - 4189    
Direction L1: <<            Initial region span: 1-7,8-9,11-149 Gap history (edge excluded): 7-11 -> 9-11
Alt. candidates: [], []                                                                                               
Model 1BP/2BP comparison:   2BP vs 1BP: 8.67e-02                                                                      
Rec. model vs L1: 2.74e-07  Rec. model vs L2: 6.30e-221                                                        
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	7	12.929009	None	None	None	*	*	*

|||||

LU.2.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LU.2.1.1	49	9	7.467971	NaN	NaN	NaN	*	*	*
MC.36	49	9	7.467971	7.467971	-10.935941	1.000000	*	*
XBB.1.5.86	101	9	6.744670	6.744670	-9.489341	0.484325	*	*
FL.13	151	9	6.342511	6.342511	-8.685022	0.324652	*	*
XBB.2.3	695	9	6.202173	6.202173	-8.404347	0.280832	*	*
BA.1.21.1	65	8	6.108827	-3.891173	11.782347	0.000012	*	*
BA.5.1.2	2225	9	4.344527	4.344527	-4.689053	0.043937	*	*
B.1.1.25	541	8	3.989795	-6.010205	16.020411	0.000001		*
EG.5.1.4	1717	9	3.911457	3.911457	-3.822914	0.028439	*	*
BA.5.2	49968	9	3.872117	3.872117	-3.744233	0.027324	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	11	314.726951	NaN	NaN	NaN	*	*	*
LF.7	58	11	302.739018	305.704624	-271.409249	6.459233e-06		*
XFG.2	500	11	297.915815	300.907665	-261.815330	5.342431e-08		*
XFG.3.1	87	11	270.847887	273.722152	-207.444304	8.303705e-20		*
XFG.1	14	11	253.668374	256.704482	-173.408964	3.386502e-27		*
LF.7.1	165	12	221.056551	214.043766	-88.087531	1.006349e-45		*
LF.7.7.1	188	12	217.477068	210.448392	-80.896784	2.763504e-47		*
LF.7.1.8	44	12	214.211779	207.178378	-74.356755	1.050309e-48		*
LF.7.6	15	12	198.977624	192.013733	-44.027466	2.724214e-55		*
LF.7.3	54	12	195.530560	188.490818	-36.981636	8.023304e-57		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3754_A|G, 4184_G|A, 4206_C|T, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16394_C|T, 16600_T|C, 17410_C|T, 17825_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28805_G|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

 Case 58 (XFG): OZ263370



Target: 530 samples         Number of changes: 150                                                             
BC: XFG.3 + LU.2.1.1 + XFG.3 BC BR: 7-8, 9-10                   BC BR coord: 3566 - 3567, 4188 - 4189    
Direction L1: <<            Initial region span: 1-7,8-9,11-150 Gap history (edge excluded): 7-11 -> 9-11
Alt. candidates: [], []                                                                                               
Model 1BP/2BP comparison:   2BP vs 1BP: 8.67e-02                                                                      
Rec. model vs L1: 2.74e-07  Rec. model vs L2: 6.37e-221                                                        
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	7	12.929009	None	None	None	*	*	*

|||||

LU.2.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LU.2.1.1	49	9	7.467971	NaN	NaN	NaN	*	*	*
MC.36	49	9	7.467971	7.467971	-10.935941	1.000000	*	*
XBB.1.5.86	101	9	6.744670	6.744670	-9.489341	0.484325	*	*
FL.13	151	9	6.342511	6.342511	-8.685022	0.324652	*	*
XBB.2.3	695	9	6.202173	6.202173	-8.404347	0.280832	*	*
BA.1.21.1	65	8	6.108827	-3.891173	11.782347	0.000012	*	*
BA.5.1.2	2225	9	4.344527	4.344527	-4.689053	0.043937	*	*
B.1.1.25	541	8	3.989795	-6.010205	16.020411	0.000001		*
EG.5.1.4	1717	9	3.911457	3.911457	-3.822914	0.028439	*	*
BA.5.2	49968	9	3.872117	3.872117	-3.744233	0.027324	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	11	316.228088	NaN	NaN	NaN	*	*	*
LF.7	58	11	304.248505	307.214112	-274.428224	6.524149e-06		*
XFG.2	500	11	299.421298	302.413148	-264.826297	5.369210e-08		*
XFG.3.1	87	11	272.334253	275.208518	-210.417036	8.221082e-20		*
XFG.1	14	11	255.177861	258.213970	-176.427940	3.420537e-27		*
LF.7.1	165	12	222.566038	215.553253	-91.106506	1.016463e-45		*
LF.7.7.1	188	12	218.986556	211.957879	-83.915759	2.791277e-47		*
LF.7.1.8	44	12	215.721266	208.687865	-77.375731	1.060865e-48		*
LF.7.6	15	12	200.487112	193.523220	-47.046441	2.751593e-55		*
LF.7.3	54	12	197.040048	190.000306	-40.000612	8.103939e-57		*

Target sequence

 Case 58 (XFG): OZ276205



Target: 530 samples         Number of changes: 154                                                                
BC: XFG.3 + LU.2.1.1 + XFG.3 BC BR: 9-10, 11-12                   BC BR coord: 3566 - 3567, 4188 - 4189     
Direction L1: <<            Initial region span: 1-9,10-11,13-154 Gap history (edge excluded): 9-13 -> 11-13
Alt. candidates: [], []                                                                                                  
Model 1BP/2BP comparison:   2BP vs 1BP: 4.37e-06                                                                         
Rec. model vs L1: 2.74e-07  Rec. model vs L2: 4.42e-223                                                           
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	9	17.865815	None	None	None	*	*	*

|||||

LU.2.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LU.2.1.1	49	11	7.467971	NaN	NaN	NaN	*	*	*
MC.36	49	11	7.467971	7.467971	-10.935941	1.000000	*	*
XBB.1.5.86	101	11	6.744670	6.744670	-9.489341	0.484325	*	*
FL.13	151	11	6.342511	6.342511	-8.685022	0.324652	*	*
XBB.2.3	695	11	6.202173	6.202173	-8.404347	0.280832	*	*
BA.1.21.1	65	10	6.108827	-3.891173	11.782347	0.000012	*	*
BA.5.1.2	2225	11	4.344527	4.344527	-4.689053	0.043937	*	*
B.1.1.25	541	10	3.989795	-6.010205	16.020411	0.000001		*
EG.5.1.4	1717	11	3.911457	3.911457	-3.822914	0.028439	*	*
BA.5.2	49968	11	3.872117	3.872117	-3.744233	0.027324	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	13	293.481844	NaN	NaN	NaN	*	*	*
LF.7	58	13	279.815429	287.949524	-227.899047	1.515144e-06		*
XFG.2	500	13	276.065493	281.917806	-215.835611	3.644670e-09		*
XFG.3.1	87	13	263.968420	270.792602	-193.585203	5.371952e-14		*
XFG.1	14	13	230.366719	236.669155	-125.338309	8.125178e-29		*
LF.7.1	165	14	197.954595	195.098146	-42.196291	7.181436e-47		*
LF.7.7.1	188	14	189.187922	185.381201	-22.762401	4.313889e-51		*
LF.7.1.8	44	14	177.294123	172.846222	2.307556	1.552343e-56		*
LF.7.6	15	14	176.200698	173.686904	0.626193	3.595795e-56		*
LF.7.3	54	14	173.078672	169.208093	9.583814	4.095691e-58		*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3754_A|G, 4184_G|A, 4206_C|T, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16394_C|T, 16600_T|C, 17410_C|T, 17825_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26842_G|A, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28005_C|T, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28805_G|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29734_29759

 Case 58 (XFG): OZ277109



Target: 530 samples         Number of changes: 155                                                          
BC: XFG.3 + KP.4.1.1 + XFG.3 BC BR: 3-4, 7-8                   BC BR coord: 241 - 242, 2789 - 2790    
Direction L1: <<            Initial region span: 1-3,5-7,8-155 Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []                                                                                            
Model 1BP/2BP comparison:   2BP vs 1BP: 6.89e-02                                                                   
Rec. model vs L1: 1.32e-08  Rec. model vs L2: 5.57e-212                                                     
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	3	4.941372	None	None	None	*	*	*

|||||

KP.4.1.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.4.1.1	12	5	9.890930	NaN	NaN	NaN	*	*	*
JN.13	15	5	9.156961	-0.843039	11.686078	0.479505	*	*
MC.33	31	5	8.718706	-1.281294	12.562588	0.310367	*	*
MD.1	19	5	7.821960	-2.178040	14.356080	0.126186	*	*
KP.2	1589	4	7.812810	7.812810	-5.625620	2765.564355	*	*
MC.36.2	24	6	7.600059	-10.920705	31.841410	0.000020	*	*
KP.2.3.13	25	5	7.547523	-2.452477	14.904954	0.096328	*	*
XFJ.1	59	5	7.330428	-2.669572	15.339144	0.077305	*	*
LF.9	48	5	6.874145	-3.125855	16.251711	0.049046	*	*
LB.1.7.1	97	5	6.864110	-3.135890	16.271781	0.048558	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	8	307.334080	NaN	NaN	NaN	*	*	*
LF.7	58	8	295.723596	300.896650	-249.793300	1.142165e-05	*	*
XFG.2	500	8	281.982221	284.845246	-217.690493	1.222651e-12		*
XFG.3.1	87	8	275.096664	279.051146	-206.102293	3.720196e-15		*
XFG.1	14	11	256.109583	250.461570	-148.923141	1.425892e-27
LF.7.1	165	17	224.704626	209.311326	-66.622651	1.918089e-45
LF.7.7.1	188	17	215.542400	190.391563	-28.783126	1.164172e-53
LF.7.6	15	17	202.560510	187.479320	-22.958639	6.341911e-55
LF.7.3	54	17	199.324167	194.336739	-36.673478	6.016014e-52
LF.7.2.1	67	17	195.749346	180.075747	-8.151494	3.857176e-58

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3096_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 7842_A|G,
7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11187_T|C, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T,
12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15613_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25613_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T,
26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29734_29759

 Case 58 (XFG): OZ277275



Target: 530 samples        Number of changes: 155                                               
BC: LB.1.3 + LF.7          BC BR: 7-8                    BC BR coord: 685 - 686          
Direction L1: <<           Initial region span: 1-3,8-155 Gap history (edge excluded): 3-8
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 5.97e-142 Rec. model vs L2: 6.86e-12                                           
Flags: Model_2BP_Bad_L1_opp

LB.1.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LB.1.3	778	3	8.908186	NaN	NaN	NaN	*	*	*
FL.2.3	614	3	4.892847	-17.217623	50.435246	3.305807e-08		*
XBB.1.5.13	2132	4	2.404054	-0.688856	17.377713	4.990744e-01	*	*
BA.4.6	19369	6	1.969609	-8.030391	32.060781	3.239245e-04	*
BA.5.1	53705	7	1.728110	1.728110	12.543781	5.612521e+00	*
BA.4	10442	6	0.589038	-9.410962	34.821924	8.149246e-05	*
BA.2	443141	6	0.155509	-0.347806	16.695611	7.011734e-01	*
BA.2.9	75328	6	0.069722	-0.881665	17.763331	4.127142e-01	*
BA.2.12.1	107150	6	-0.688939	-0.894092	17.788184	4.065697e-01	*
BQ.1.1	36940	7	-0.868500	-0.868500	17.736999	4.168620e-01	*

|||||

LF.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	8	316.180071	NaN	NaN	NaN	*	*	*
XFG.3	480	5	309.875086	308.960029	-265.920058	7.318024e-04	*
XFG.2	500	9	306.211341	302.285967	-252.571933	9.235878e-07		*
XFG.1	14	8	289.021195	289.021195	-226.042390	1.601629e-12		*
XFG.3.1	87	8	266.528790	266.528790	-181.057580	2.737026e-22		*
LF.7.1	165	16	243.057180	236.047856	-120.095713	1.584832e-35
LF.7.7.1	188	16	224.543813	208.690917	-65.381834	2.078194e-47
LF.7.7.2	239	16	216.171252	190.766192	-29.532384	3.411596e-55
LF.7.2.1	67	16	213.415984	206.391862	-60.783724	2.083574e-48
LF.7.3	54	16	209.578371	202.523741	-53.047482	4.367779e-50

Target sequence

, 21_C|T, 44_C|T, 88_G|A, 121_C|T, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4230_C|T, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 16887_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A,
23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 28961_C|T, 29409_C|T, 29510_A|C, 29734_29759,
29762_C|T

 Case 58 (XFG): OZ263370



Target: 530 samples         Number of changes: 150                                                             
BC: XFG.3 + LU.2.1.1 + XFG.3 BC BR: 7-8, 9-10                   BC BR coord: 3566 - 3567, 4188 - 4189    
Direction L1: <<            Initial region span: 1-7,8-9,11-150 Gap history (edge excluded): 7-11 -> 9-11
Alt. candidates: [], []                                                                                               
Model 1BP/2BP comparison:   2BP vs 1BP: 8.67e-02                                                                      
Rec. model vs L1: 2.74e-07  Rec. model vs L2: 6.37e-221                                                        
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	7	12.929009	None	None	None	*	*	*

|||||

LU.2.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LU.2.1.1	49	9	7.467971	NaN	NaN	NaN	*	*	*
MC.36	49	9	7.467971	7.467971	-10.935941	1.000000	*	*
XBB.1.5.86	101	9	6.744670	6.744670	-9.489341	0.484325	*	*
FL.13	151	9	6.342511	6.342511	-8.685022	0.324652	*	*
XBB.2.3	695	9	6.202173	6.202173	-8.404347	0.280832	*	*
BA.1.21.1	65	8	6.108827	-3.891173	11.782347	0.000012	*	*
BA.5.1.2	2225	9	4.344527	4.344527	-4.689053	0.043937	*	*
B.1.1.25	541	8	3.989795	-6.010205	16.020411	0.000001		*
EG.5.1.4	1717	9	3.911457	3.911457	-3.822914	0.028439	*	*
BA.5.2	49968	9	3.872117	3.872117	-3.744233	0.027324	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	11	316.228088	NaN	NaN	NaN	*	*	*
LF.7	58	11	304.248505	307.214112	-274.428224	6.524149e-06		*
XFG.2	500	11	299.421298	302.413148	-264.826297	5.369210e-08		*
XFG.3.1	87	11	272.334253	275.208518	-210.417036	8.221082e-20		*
XFG.1	14	11	255.177861	258.213970	-176.427940	3.420537e-27		*
LF.7.1	165	12	222.566038	215.553253	-91.106506	1.016463e-45		*
LF.7.7.1	188	12	218.986556	211.957879	-83.915759	2.791277e-47		*
LF.7.1.8	44	12	215.721266	208.687865	-77.375731	1.060865e-48		*
LF.7.6	15	12	200.487112	193.523220	-47.046441	2.751593e-55		*
LF.7.3	54	12	197.040048	190.000306	-40.000612	8.103939e-57		*

Target sequence

 Case 58 (XFG): OZ282610



Target: 530 samples        Number of changes: 152                                               
BC: JN.11 + XFG.2          BC BR: 5-6                    BC BR coord: 2067 - 2068        
Direction L1: <<           Initial region span: 1-5,7-152 Gap history (edge excluded): 5-7
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 1.07e-235 Rec. model vs L2: 1.16e-23                                           
Flags: Model_2BP_Bad_L1_opp

JN.11 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.11	67	5	9.433251	NaN	NaN	NaN	*	*	*
KP.2.3.10	10	4	8.417788	-1.582212	19.164424	1.645304e-05	*	*
PL.1.1	12	4	8.235466	-1.764534	19.529067	1.367420e-05	*	*
PD.2	21	4	7.675851	-8.934158	33.868317	1.051987e-08		*
KP.4.2.4	22	4	7.629331	-10.408730	36.817461	2.406722e-09		*
KR.1.4	24	4	7.408788	-9.835735	35.671469	4.277060e-09		*
KP.3.1.2	28	4	7.277693	-2.722307	21.444614	5.261997e-06		*
JN.1.69	32	4	7.254637	-2.745363	21.490726	5.132078e-06		*
KP.3.1	1957	5	7.210993	7.210993	1.578014	1.080674e-01	*	*
JN.1.50.2	33	4	7.162322	-2.837678	21.675356	4.666972e-06		*

|||||

XFG.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.2	500	7	320.737083	NaN	NaN	NaN	*	*	*
XFG.3	480	8	313.613273	293.613273	-247.226546	7.470942e-12		*
LF.7	58	8	313.571870	293.571870	-247.143740	7.142202e-12		*
XFG.3.1	87	8	281.566276	261.566276	-183.132551	8.999891e-26		*
XFG.1	14	8	264.571728	244.571728	-149.143455	3.744575e-33		*
LF.7.1	165	14	222.566038	201.941555	-63.883111	1.146644e-51
LF.7.7.1	188	14	218.986556	210.385030	-80.770060	5.333910e-48
LF.7.1.8	44	14	215.721266	195.115133	-50.230265	1.245572e-54
LF.7.6	15	14	200.487112	179.880978	-19.761956	3.012260e-61
LF.7.3	54	14	197.040048	176.358064	-12.716127	8.916120e-63

Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 1684_C|T, 2334_C|T, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13118_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22088_C|T, 22107_A|G, 22132_G|T,
22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

 Case 58 (XFG): OZ284632



Target: 530 samples        Number of changes: 143                                               
BC: BQ.1.1.35 + XFG.3      BC BR: 4-5                    BC BR coord: 685 - 686          
Direction L1: <<           Initial region span: 1-4,9-143 Gap history (edge excluded): 4-9
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 2.23e-10                                           
Flags: Model_2BP_Bad_L1_opp

BQ.1.1.35 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
BQ.1.1.35	191	4	10.486205	NaN	NaN	NaN	*	*	*
ET.1	78	3	7.434339	-2.565661	13.131321	0.000002		*
KP.3.1.4	511	7	7.427846	2.741159	2.517682	0.000433	*
XEC.39	155	5	6.963453	3.342570	1.314859	0.000793	*	*
LB.1.3.1	292	7	6.759817	2.065162	3.869677	0.000220	*
KP.2.2	1334	7	6.735397	2.058892	3.882216	0.000219	*
MC.16	917	6	6.418927	1.730826	4.538348	0.000158	*
KP.3.1	1957	7	6.411016	1.728378	4.543244	0.000158	*
XEC.2	921	7	6.064512	1.375780	5.248439	0.000111	*
XBC.1	44	4	5.867514	5.867514	-3.735028	0.009902	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	9	278.075549	NaN	NaN	NaN	*	*	*
XFG.2	500	9	270.818475	257.964145	-167.928290	3.736299e-07		*
LF.7	58	9	247.857314	242.548371	-137.096742	7.547311e-14		*
XFG.3.1	87	9	233.774196	228.482644	-108.965289	5.880853e-20		*
XFG.1	14	9	187.790145	182.498594	-16.997187	6.286495e-40		*
LF.7.1	165	13	178.996898	171.987574	4.024852	1.713853e-44
LF.7.7.1	188	13	143.224718	127.371822	93.256356	7.173875e-64
LF.7.3.1	26	13	139.050423	132.032423	83.935153	7.578200e-62
JN.1.16.1	466	13	135.350871	128.315666	91.368669	1.845704e-63
LF.7.3	54	13	134.060531	127.005901	93.988198	4.980080e-64

Target sequence

, 241_C|T, 601_C|T, 670_T|G, 683_C|T, 897_C|A, 2790_C|T, 3037_C|T, 3145_G|A, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11020_C|T, 11042_G|T, 11083_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15738_C|T, 15756_T|A, 16600_T|C, 16887_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21653_T|C, 21711_C|T,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22606_A|G, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28881_G|A, 28882_G|A,
28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29762_C|T

 Case 58 (XFG): OZ284870



Target: 530 samples       Number of changes: 140                                                                    
BC: LF.7 + HK.13 + LF.7   BC BR: 129-130, 134-135                   BC BR coord: 27915 - 27916, 28880 - 28881
Direction L1: >>          Initial region span: 1-129,130-134,135-140 Gap history (edge excluded): 129-135 ->  
Alt. candidates: [], []                                                                                                    
Model 1BP/2BP comparison: 2BP vs 1BP: 2.55e-03                                                                             
Rec. model vs L1: 1.02e-15 Rec. model vs L2: 0.00e+00                                                                
Flags: Model_2BP_Best

LF.7 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	129	279.782631	NaN	NaN	NaN	*	*	*
XFG.3	480	140	254.107420	255.211820	-172.423641	3.538760e-15
XFG.3.1	87	129	229.930731	242.296025	-146.592049	8.708390e-21		*
XFG.2	500	103	228.717189	237.752784	-137.505569	9.294819e-23
XFG.1	14	103	170.141484	177.670054	-17.340109	7.475788e-49
LF.7.1	165	140	155.652251	149.265249	39.469501	3.447643e-61
LF.7.3.1	26	129	149.543813	144.685647	48.628705	3.535522e-63		*
LF.7.1.8	44	129	145.949746	141.142250	55.715501	1.020656e-64		*
LF.7.9	20	73	145.140273	132.767805	72.464389	2.365020e-68
LF.7.7.1	188	133	142.635628	144.292390	49.415220	2.381810e-63

|||||

HK.13 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
HK.13	165	130	10.169244	NaN	NaN	NaN	*	*	*
FY.8.1	29	131	9.130739	-0.869261	13.738522	0.000016	*	*
FY.4.1	61	131	8.549246	-1.450754	14.901508	0.000009		*
FY.8	23	130	8.410314	8.410314	-4.820627	0.172045	*	*
FL.1	118	130	8.290629	8.290629	-4.581259	0.152590	*	*
HK.19	25	131	7.758518	-2.241482	16.482963	0.000004		*
XFG.3	480	131	7.718840	-2.281160	16.562320	0.000004		*
HK.8	39	131	7.699095	-2.300905	16.601810	0.000004		*
EG.9.1	32	131	7.183154	-2.816846	17.633692	0.000002		*
EG.5.1.2	69	131	7.065371	-2.934629	17.869258	0.000002		*

|||||

LF.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	135	8.703627	None	None	None	*	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C,
17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21641_G|T, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G,
22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22883_C|A, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23758_C|T,
23854_C|A, 23948_G|T, 24034_C|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25273_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28093_C|T, 28271_A|T, 28297_T|C, 28311_C|T, 28878_G|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A,
29409_C|T, 29510_A|C

 Case 58 (XFG): OZ285842



Target: 530 samples        Number of changes: 150                                               
BC: JN.11 + LF.7           BC BR: 4-5                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-4,7-150 Gap history (edge excluded): 4-7
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 1.22e-227 Rec. model vs L2: 4.18e-08                                           
Flags: Model_2BP_Bad_L1_opp

JN.11 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.11	67	4	8.712905	NaN	NaN	NaN	*	*	*
KP.2.3.10	10	4	8.417788	8.417788	-8.835576	0.744532	*	*
PL.1.1	12	4	8.235466	8.235466	-8.470933	0.618783	*	*
PD.2	21	4	7.675851	7.675851	-7.351701	0.353455	*	*
KP.4.2.4	22	4	7.629331	7.629331	-7.258661	0.337902	*	*
KR.1.4	24	4	7.408788	7.408788	-6.817576	0.271173	*	*
KP.3.1.2	28	4	7.277693	7.277693	-6.555386	0.238115	*	*
JN.1.69	32	4	7.254637	7.254637	-6.509274	0.232236	*	*
JN.1.50.2	33	4	7.162322	7.162322	-6.324644	0.211189	*	*
LP.8.1.10	32	4	7.156197	7.156197	-6.312394	0.210136	*	*

|||||

LF.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	7	334.007833	NaN	NaN	NaN	*	*	*
XFG.3	480	7	333.322187	313.322187	-282.644374	5.015761e-01	*	*
XFG.2	500	7	328.181516	309.140532	-274.281065	7.673365e-03	*	*
XFG.3.1	87	7	291.566276	271.566276	-199.132551	3.684433e-19		*
XFG.1	14	7	286.429076	266.429076	-188.858152	2.169045e-21		*
LF.7.1	165	13	242.649646	222.025163	-100.050326	1.125698e-40
LF.7.7.1	188	13	228.986556	209.020063	-74.040126	2.531759e-46
LF.7.1.8	44	13	225.721266	205.115133	-66.230265	5.099204e-48
LF.7.6	15	13	210.487112	189.880978	-35.761956	1.233179e-54
LF.7.3.1	26	13	209.990938	189.345583	-34.691167	7.222348e-55

Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 1096_A|G, 2334_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16475_G|A, 16600_T|C, 16887_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

 Case 58 (XFG): OZ263370



Target: 530 samples         Number of changes: 150                                                             
BC: XFG.3 + LU.2.1.1 + XFG.3 BC BR: 7-8, 9-10                   BC BR coord: 3566 - 3567, 4188 - 4189    
Direction L1: <<            Initial region span: 1-7,8-9,11-150 Gap history (edge excluded): 7-11 -> 9-11
Alt. candidates: [], []                                                                                               
Model 1BP/2BP comparison:   2BP vs 1BP: 8.67e-02                                                                      
Rec. model vs L1: 2.74e-07  Rec. model vs L2: 6.37e-221                                                        
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	7	12.929009	None	None	None	*	*	*

|||||

LU.2.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LU.2.1.1	49	9	7.467971	NaN	NaN	NaN	*	*	*
MC.36	49	9	7.467971	7.467971	-10.935941	1.000000	*	*
XBB.1.5.86	101	9	6.744670	6.744670	-9.489341	0.484325	*	*
FL.13	151	9	6.342511	6.342511	-8.685022	0.324652	*	*
XBB.2.3	695	9	6.202173	6.202173	-8.404347	0.280832	*	*
BA.1.21.1	65	8	6.108827	-3.891173	11.782347	0.000012	*	*
BA.5.1.2	2225	9	4.344527	4.344527	-4.689053	0.043937	*	*
B.1.1.25	541	8	3.989795	-6.010205	16.020411	0.000001		*
EG.5.1.4	1717	9	3.911457	3.911457	-3.822914	0.028439	*	*
BA.5.2	49968	9	3.872117	3.872117	-3.744233	0.027324	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	11	316.228088	NaN	NaN	NaN	*	*	*
LF.7	58	11	304.248505	307.214112	-274.428224	6.524149e-06		*
XFG.2	500	11	299.421298	302.413148	-264.826297	5.369210e-08		*
XFG.3.1	87	11	272.334253	275.208518	-210.417036	8.221082e-20		*
XFG.1	14	11	255.177861	258.213970	-176.427940	3.420537e-27		*
LF.7.1	165	12	222.566038	215.553253	-91.106506	1.016463e-45		*
LF.7.7.1	188	12	218.986556	211.957879	-83.915759	2.791277e-47		*
LF.7.1.8	44	12	215.721266	208.687865	-77.375731	1.060865e-48		*
LF.7.6	15	12	200.487112	193.523220	-47.046441	2.751593e-55		*
LF.7.3	54	12	197.040048	190.000306	-40.000612	8.103939e-57		*

Target sequence

 Case 58 (XFG): OZ286915



Target: 530 samples       Number of changes: 135                                                                  
BC: XFG.3 + CP.5 + XFG.3  BC BR: 16-17, 26-27                   BC BR coord: 7842 - 7843, 11307 - 11308    
Direction L1: <<          Initial region span: 1-16,17-21,35-135 Gap history (edge excluded): 16-35 -> 21-35
Alt. candidates: [], []                                                                                                  
Model 1BP/2BP comparison: 2BP vs 1BP: 2.65e-11                                                                           
Rec. model vs L1: 2.72e-52 Rec. model vs L2: 0.00e+00                                                              
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	16	32.463016	None	None	None	*	*	*

|||||

CP.5 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
CP.5	75	21	9.955291	NaN	NaN	NaN	*	*	*
GU.1	74	20	9.843387	-10.014339	46.028679	0.000001		*
XBB.1.5.41	44	20	9.843387	-10.014339	46.028679	0.000001		*
DV.5	17	20	9.312759	1.553633	22.892735	0.118837	*	*
BA.5.1.22	4997	26	9.302971	9.302971	7.394059	275.889383	*
BQ.1.13	999	26	9.177364	9.177364	7.645272	242.257207	*
BA.5.2.22	994	26	8.899675	8.899675	8.200651	184.011821	*
BE.1	8190	27	8.627139	6.216802	13.566396	12.553506	*
DN.2	895	26	8.007393	8.007393	9.985213	75.188628	*
BF.7	11554	27	7.718461	6.590511	12.818978	18.265244	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	35	211.076442	NaN	NaN	NaN	*	*	*
LF.7	58	35	207.482856	193.116410	-76.232819	2.839438e-13		*
XFG.2	500	35	197.290861	182.762504	-55.525009	9.084155e-18		*
XFG.3.1	87	39	191.688029	170.702727	-31.405455	5.256457e-23
XFG.1	14	39	189.636519	163.254528	-16.509056	3.056323e-26
LF.7.7.1	188	39	165.425663	142.106791	25.786418	1.994669e-35
LF.7.1	165	35	156.111811	124.906057	60.187887	6.760920e-43		*
KP.3	769	18	152.632080	162.092837	-14.185675	9.581149e-27
KP.3.1	1957	36	150.309901	120.997031	68.005937	1.354922e-44		*
LF.7.3	54	39	150.119738	105.797158	98.405685	3.393425e-51

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 5622_C|T, 6183_A|G, 7113_C|T, 7842_A|G, 8818_C|T, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10039_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11288_11296, 11681_C|T, 11727_G|A, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 17410_C|T, 18163_A|G, 18894_C|T, 19955_C|T,
20055_A|G, 20178_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C,
22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): OZ286929



Target: 530 samples       Number of changes: 154                                                                          
BC: LF.7 + XDD.1.1 + LF.7 BC BR: 141-142, 147-148                   BC BR coord: 27915 - 27916, 28880 - 28881      
Direction L1: >>          Initial region span: 1-141,143-147,148-154 Gap history (edge excluded): 141-148 -> 141-143
Alt. candidates: [], []                                                                                                          
Model 1BP/2BP comparison: 2BP vs 1BP: 1.27e-06                                                                                   
Rec. model vs L1: 1.65e-07 Rec. model vs L2: 0.00e+00                                                                      
Flags: Model_2BP_Best

LF.7 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	141	298.898197	NaN	NaN	NaN	*	*	*
XFG.3	480	141	297.792045	311.334099	-286.668198	3.706174e+00	*	*
XFG.2	500	141	288.893236	302.457353	-268.914705	5.156924e-04	*	*
XFG.3.1	87	141	263.743179	276.700095	-217.400191	3.366173e-15		*
XFG.1	14	141	245.223539	258.908693	-181.817386	6.324665e-23		*
LF.7.1	165	141	208.084215	217.262826	-98.525652	5.186135e-41		*
LF.7.6	15	141	205.217225	202.733078	-69.466157	2.538312e-47		*
LF.7.7.1	188	141	202.099682	206.410565	-76.821130	1.001330e-45		*
LF.7.1.8	44	141	197.600079	195.085761	-54.171522	1.208349e-50		*
LF.7.3	54	141	193.829884	191.451098	-46.902196	3.188099e-52		*

|||||

XDD.1.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XDD.1.1	29	143	13.385163	NaN	NaN	NaN	*	*	*
JG.3	1482	143	10.138247	0.138247	17.723506	3.896856e-02	*	*
HK.3	1830	143	9.256169	-0.743831	19.487662	1.608288e-02	*	*
JN.1.3	111	145	8.464940	-16.336019	50.672039	2.727174e-09
XBB.1.5.43	48	145	8.201786	-11.033084	40.066167	5.463533e-07
GK.2.1	255	143	7.855661	-8.235089	34.470179	8.984587e-06		*
BW.1	131	145	7.218843	-12.016026	42.032053	2.050525e-07
XBB.1.16.6	4784	142	6.553074	6.553074	4.893853	2.380748e+01	*	*
BA.2.76	427	145	6.030217	-13.204653	44.409305	6.238132e-08
BA.2.36	3016	145	5.869129	-13.366736	44.733472	5.315785e-08

|||||

LF.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	148	11.12495	None	None	None	*	*	*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4822_A|G, 5239_C|T, 6183_A|G, 6351_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 9989_A|G, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25703_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28268_A|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28467_A|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29734_29759

 Case 58 (XFG): OZ286968



Target: 530 samples        Number of changes: 151                                               
BC: XEK.6 + XFG.3          BC BR: 6-7                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-6,8-151 Gap history (edge excluded): 6-8
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  1BP vs 2BP: 2.00e-01                                                        
Rec. model vs L1: 1.10e-245 Rec. model vs L2: 3.00e-09                                           
Flags: Model_1BP_Best

XEK.6 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEK.6	23	6	16.273655	NaN	NaN	NaN	*	*	*
XEK.7	12	6	15.403708	15.403708	-18.807416	0.418952	*	*
XEK.2	67	6	15.085032	15.085032	-18.170063	0.304221	*	*
XEK.1	88	6	13.684686	13.684686	-15.369373	0.075020	*	*
XEK.1.1	11	6	12.997514	12.997514	-13.995028	0.037817	*	*
KP.2.3.5	89	6	12.724723	12.724723	-13.449447	0.028725	*	*
PF.2.1	37	6	12.259868	12.259868	-12.519735	0.018043	*	*
LP.8.1.7	42	6	12.225238	12.225238	-12.450475	0.017422	*	*
KP.2.2	1334	7	12.190723	8.722390	-5.444779	0.000523	*	*
LF.9	48	6	12.151112	12.151112	-12.302224	0.016163	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	8	348.462493	NaN	NaN	NaN	*	*	*
XFG.2	500	8	340.821226	323.282596	-306.565192	2.567919e-07		*
LF.7	58	8	336.350487	326.350487	-312.700975	5.504195e-06		*
XFG.3.1	87	8	304.123042	294.123042	-248.246084	5.566140e-20		*
XFG.1	14	8	287.190678	277.190678	-214.381355	2.459105e-27		*
LF.7.1	165	14	254.384274	243.759791	-147.519582	7.452682e-42
LF.7.7.1	188	14	236.607347	217.165042	-94.330084	2.100152e-53
LF.7.1.8	44	14	224.724215	214.118082	-88.236163	9.995951e-55
LF.7.6	15	14	223.630791	213.024657	-86.049313	3.344042e-55
LF.7.3.1	26	14	222.884140	212.238785	-84.477570	1.525283e-55

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 593_C|T, 670_T|G, 897_C|A, 979_T|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25708_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): OZ287971



Target: 530 samples            Number of changes: 144                                                             
BC: XFG.3 + XBB.1.16.22 + XFG.3 BC BR: 4-5, 8-9                    BC BR coord: 896 - 897, 3176 - 3177      
Direction L1: <<               Initial region span: 1-4,5-8,10-144 Gap history (edge excluded): 4-10 -> 8-10
Alt. candidates: [], []                                                                                                  
Model 1BP/2BP comparison:      2BP vs 1BP: 6.27e-02                                                                      
Rec. model vs L1: 3.57e-15     Rec. model vs L2: 0.00e+00                                                         
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	4	4.53194	None	None	None	*	*	*

|||||

XBB.1.16.22 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XBB.1.16.22	25	8	8.182764	NaN	NaN	NaN	*	*	*
NL.4	115	9	8.012209	4.437504	1.124991	2.363563e-02	*	*
GN.1.1	93	8	7.347076	7.347076	-4.694153	4.317105e-01	*	*
JN.1.9	576	9	6.174414	2.599710	4.800580	3.753750e-03	*	*
AY.71	260	5	5.908262	-0.407936	10.815872	1.850286e-04	*
AY.73	462	5	5.908262	-14.087852	38.175704	2.118802e-10
AY.72	300	5	5.908262	-14.087852	38.175704	2.118802e-10
B.1.1.181	17	5	5.908262	-14.087852	38.175704	2.118802e-10
AY.2	1597	5	5.907009	-21.536087	53.072174	1.238135e-13
AY.38	560	5	5.897490	-14.098624	38.197248	2.097720e-10

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	10	236.270134	NaN	NaN	NaN	*	*	*
LF.7	58	10	233.697884	228.383026	-110.766052	4.118589e-06		*
XFG.2	500	10	230.267352	224.873192	-103.746384	1.231331e-07		*
XFG.3.1	87	9	229.822136	224.540955	-103.081910	8.808179e-08		*
XFG.1	14	10	182.893469	177.525502	-9.051003	3.361484e-28		*
LF.7.1	165	12	150.222089	147.507258	50.985483	3.083264e-41
LF.7.3.1	26	12	144.392309	130.100918	85.798164	8.513640e-49
LF.7.1.8	44	12	142.683653	128.322753	89.354495	1.442921e-49
LF.7.7.1	188	12	141.151123	128.739889	88.520223	2.185117e-49
LF.7.9	20	12	131.014800	116.828770	112.342460	1.469019e-54

Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2509_C|T, 2790_C|T, 3037_C|T, 3176_C|T, 3431_G|T, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12116_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 18981_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22259_A|G, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 27887_A|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A,
28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): OZ287981



Target: 530 samples        Number of changes: 139                                           
BC: JN.1.61 + XFG.2        BC BR: 4-5                    BC BR coord: 2067 - 2068    
Direction L1: <<           Initial region span: 1-4,5-139 Gap history (edge excluded):
Alt. candidates: [], []                                                                            
Model 1BP/2BP comparison:  -                                                                       
Rec. model vs L1: 4.21e-154 Rec. model vs L2: 1.46e-16                                       
Flags: Model_2BP_Bad_L1_opp

JN.1.61 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.61	13	4	8.056002	NaN	NaN	NaN	*	*	*
LF.7.6	15	4	7.912902	7.912902	-3.825803	0.869358	*	*
MC.5	19	4	7.676513	7.676513	-3.353026	0.683861	*	*
JN.1.9	576	4	7.611185	7.611185	-3.222370	0.640824	*	*
XFG.3.1	87	4	7.541338	7.541338	-3.082676	0.597501	*	*
KP.3.5	345	4	7.429557	1.360203	9.279594	0.001237	*	*
JN.1.40	26	4	7.323635	7.323635	-2.647269	0.481909	*	*
XEC.2.3	28	4	7.288747	7.288747	-2.577494	0.465334	*	*
KP.3.1.11	31	4	7.186965	-2.161221	16.322441	0.000037	*	*
KP.2.27	73	4	7.009846	7.009846	-2.019692	0.351692	*	*

|||||

XFG.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.2	500	5	268.451318	NaN	NaN	NaN	*	*	*
XFG.3	480	3	266.120225	261.420618	-184.841236	8.849318e-04	*
XFG.3.1	87	1	263.645367	256.104029	-174.208058	4.351456e-06
LF.7	58	3	263.284930	258.570676	-179.141352	5.118828e-05	*
XFG.1	14	3	212.337916	207.623663	-77.247325	3.837409e-27
LF.7.1	165	1	184.727660	177.856903	-17.713807	4.519511e-40
LF.7.3.1	26	3	165.604825	160.929792	16.140417	2.016774e-47
LF.7.1.8	44	15	163.998212	158.490423	21.019154	1.757838e-48
LF.7.7.1	188	14	160.364115	148.132389	41.735222	5.567855e-53
LF.7.9	20	3	153.201129	148.486875	41.026250	7.940767e-53

Target sequence

, 241_C|T, 337_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 5654_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 20404_C|T, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C,
22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T,
22688_A|G, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26029_C|A, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29734_29759

 Case 58 (XFG): OZ288005



Target: 530 samples       Number of changes: 156                                                   
BC: JN.1 + XFG.3          BC BR: 13-14                    BC BR coord: 3795 - 3796          
Direction L1: <<          Initial region span: 1-12,14-156 Gap history (edge excluded): 12-14
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 5.90e-06                                                            
Rec. model vs L1: 8.74e-98 Rec. model vs L2: 1.29e-14                                               
Flags: Model_1BP_Best

JN.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1	17255	12	14.844390	NaN	NaN	NaN	*	*	*
KP.2.3.10	10	6	13.966498	-7.716213	47.432427	3.599702e-10
KP.4.2.4	22	6	13.105203	-16.873398	65.746796	3.785550e-14
XEC.2.1	265	7	12.883972	1.174578	29.650843	2.613030e-06
XEC.2.2.1	46	6	12.719756	-17.254500	66.509000	2.588792e-14
MK.1	151	6	12.429824	-9.293433	50.586866	7.414489e-11
KR.1.4	24	6	11.948497	-16.978736	65.957472	3.408224e-14
JN.11	67	6	11.892484	-23.451718	78.903436	5.280108e-17
KP.3.1.2	28	6	11.663252	-10.019459	52.038918	3.591019e-11
JN.1.69	32	6	11.470297	-10.212414	52.424828	2.969626e-11

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	14	299.641562	NaN	NaN	NaN	*	*	*
LF.7	58	14	298.103700	298.103700	-266.207400	2.154557e-01	*	*
XFG.2	500	14	294.527672	294.527672	-259.055343	6.036083e-03	*	*
XFG.3.1	87	14	265.967596	265.967596	-201.935191	2.383992e-15		*
XFG.1	14	14	248.873388	248.873388	-167.746777	8.975127e-23		*
LF.7.1	165	16	215.285288	206.361865	-82.723729	3.083264e-41
LF.7.7.1	188	16	206.607347	188.853086	-47.706173	7.703460e-49
LF.7.1.8	44	16	194.724215	185.800792	-41.601585	3.630080e-50
LF.7.6	15	16	193.630791	184.707368	-39.414735	1.214405e-50
LF.7.3	54	16	190.394448	181.452332	-32.904665	4.685276e-52

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 1429_T|C, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3792_C|T, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G,
7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 18981_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21607_.|GNNNNNNNNNNN,
21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T,
22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22311_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A,
22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T,
26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29362_C|T, 29409_C|T,
29510_A|C, 29734_29759

 Case 58 (XFG): OZ288008



Target: 530 samples        Number of changes: 144                                               
BC: LD.1 + XFG.3.1         BC BR: 4-5                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-4,6-144 Gap history (edge excluded): 4-6
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 1.04e-172 Rec. model vs L2: 1.35e-07                                           
Flags: Model_2BP_Bad_L1_opp

LD.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LD.1	70	4	9.085704	NaN	NaN	NaN	*	*	*
XEC.29	135	4	8.457912	8.457912	-8.915824	0.535261	*	*
BA.5.1.17	357	3	8.456578	-1.543422	11.086845	0.000024	*	*
JN.1.29	69	4	7.971640	7.971640	-7.943281	0.327915	*	*
KP.2	1589	5	7.815486	6.243829	-4.487657	0.058426	*	*
MC.8	93	4	7.731975	7.731975	-7.463950	0.257947	*	*
XEC.39	155	4	7.208205	7.208205	-6.416409	0.153355	*	*
MC.9	298	4	6.547233	6.547233	-5.094467	0.078866	*	*
MC.2	396	4	6.252566	6.252566	-4.505133	0.059013	*	*
MC.1	932	4	6.073660	6.073660	-4.147321	0.049292	*	*

|||||

XFG.3.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3.1	87	6	216.104029	NaN	NaN	NaN	*	*	*
XFG.3	480	6	210.478161	200.478161	-38.956321	3.606563e-03	*	*
LF.7	58	6	204.955260	194.955260	-27.910520	1.437529e-05	*	*
XFG.2	500	6	193.543640	185.842548	-9.685095	1.589256e-09		*
XFG.1	14	17	167.864152	157.623663	46.752675	8.818679e-22
LF.7.3.1	26	16	134.359234	110.929792	140.140417	4.634711e-42
PY.4	10	16	131.975776	94.360777	173.278445	2.949600e-49
LF.7.1	165	17	130.995405	116.455871	129.088258	1.162786e-39
LF.7.7.1	188	16	130.364115	98.132389	165.735222	1.279538e-47
LF.7.1.8	44	17	122.052452	96.544664	168.910673	2.622386e-48

Target sequence

, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 5944_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 18912_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21676_C|T, 21711_C|T, 21811_C|T, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 26906_T|C, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28881_G|A, 28882_G|A,
28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29546_C|T, 29734_29759

 Case 58 (XFG): OZ288058



Target: 530 samples       Number of changes: 144                                                          
BC: XFG.3 + BW.1 + XFG.3  BC BR: 3-4, 5-6                   BC BR coord: 896 - 897, 2792 - 2793    
Direction L1: <<          Initial region span: 1-3,4-5,7-144 Gap history (edge excluded): 3-7 -> 5-7
Alt. candidates: [], []                                                                                          
Model 1BP/2BP comparison: 2BP vs 1BP: 2.59e-02                                                                   
Rec. model vs L1: 5.55e-09 Rec. model vs L2: 0.00e+00                                                      
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	3	4.704173	None	None	None	*	*	*

|||||

BW.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
BW.1	131	5	8.022833	NaN	NaN	NaN	*	*	*
BW.1.1.1	116	5	8.022833	8.022833	-12.045667	1.000000	*	*
BW.1.1.2	55	5	8.022833	8.022833	-12.045667	1.000000	*	*
BW.1.1	210	5	8.008445	8.008445	-12.016889	0.985112	*	*
FL.1	118	6	5.310087	3.252149	-2.504297	0.008438	*	*
XBB.2.3.19	115	5	4.376513	4.376513	-4.753027	0.025991	*	*
XBB.1.5.79	118	5	4.350761	4.350761	-4.701522	0.025349	*	*
JY.1.1	42	5	4.285164	4.285164	-4.570327	0.023754	*	*
BA.4	10442	5	4.223701	4.223701	-4.447401	0.022371	*	*
BA.2.79	46	5	4.194192	4.194192	-4.388384	0.021710	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	7	283.528307	NaN	NaN	NaN	*	*	*
XFG.2	500	7	276.945175	271.633794	-197.267588	1.367187e-03	*	*
LF.7	58	7	270.781084	265.499903	-184.999806	2.960951e-06		*
XFG.3.1	87	7	264.002856	258.721675	-171.443351	3.364454e-09		*
XFG.1	14	7	207.581325	202.300144	-58.600287	1.056866e-33		*
LF.7.1	165	12	189.445739	182.432323	-18.864645	2.480782e-42
LF.7.1.8	44	16	177.315503	165.379816	15.240367	9.769396e-50
LF.7.7.1	188	12	171.640098	155.779953	34.440094	6.616689e-54
LF.7.3.1	26	16	171.581856	164.253148	17.493704	3.171659e-50
LF.7.9	20	12	158.117910	151.048026	43.903947	5.840201e-56

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2144_G|A, 2790_C|T, 2902_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6286_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 20238_G|T, 21641_G|T, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28467_A|T, 28881_G|A,
28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): OZ288067



Target: 530 samples       Number of changes: 142                                                       
BC: XFG.3 + KP.2.3        BC BR: 112-113                    BC BR coord: 25216 - 25217          
Direction L1: >>          Initial region span: 1-112,117-142 Gap history (edge excluded): 112-117
Alt. candidates: [], []                                                                                       
Model 1BP/2BP comparison: 1BP vs 2BP: 7.19e-03                                                                
Rec. model vs L1: 2.13e-12 Rec. model vs L2: 2.91e-105                                                  
Flags: Model_1BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	112	204.434040	NaN	NaN	NaN	*	*	*
XFG.3.1	87	109	197.771630	196.677218	-105.354436	4.264566e-04	*
LF.7	58	112	190.829205	190.829205	-93.658410	1.234308e-06		*
XFG.2	500	138	189.420789	175.301596	-62.603191	2.222441e-13
XFG.1	14	112	161.065352	161.065352	-34.130704	1.460994e-19		*
LF.7.4	15	90	126.270585	107.691824	72.616352	9.642294e-43
LF.7.3.1	26	112	116.688624	116.688624	54.622752	7.813231e-39		*
LF.7.9	20	90	114.674067	104.495420	79.009160	3.950113e-44
LF.7.1	165	90	113.487679	103.272409	81.455183	1.160376e-44
LF.7.1.8	44	138	110.346683	106.082452	75.835097	1.927375e-43

|||||

KP.2.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3	4440	117	26.156199	NaN	NaN	NaN	*	*	*
XFG.3.1	87	117	23.062675	-7.225622	88.451244	8.032020e-11		*
KP.2	1589	114	22.514011	21.740280	30.519441	3.049049e+02	*
BA.2.86.1	1343	117	22.514000	10.425142	53.149716	3.716399e-03	*	*
JN.1.7	1974	117	20.286196	1.417127	71.165747	4.540766e-07		*
XFG.1	14	117	20.242476	-20.160215	114.320429	1.937428e-16		*
XFG.3	480	117	20.189990	-10.109868	94.219735	4.486268e-12		*
KP.2.2	1334	117	18.859660	-9.256657	92.513314	1.054890e-11		*
LP.8.1.1	2345	117	18.034668	-1.303536	76.607071	2.991218e-08		*
JN.1.32	436	117	17.998828	-3.390981	80.781963	3.718297e-09		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16600_T|C, 17410_C|T, 17463_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21995_21997, 22032_T|C, 22033_C|A, 22034_A|G,
22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A,
22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25445_G|T, 25584_C|T, 26028_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27754_G|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A,
29367_C|T, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): OZ288069



Target: 530 samples        Number of changes: 145                                                                          
BC: XFG.3 + XDD.1.1 + XFG.3 BC BR: 133-134, 138-139                   BC BR coord: 27915 - 27916, 28880 - 28881      
Direction L1: >>           Initial region span: 1-133,135-138,139-145 Gap history (edge excluded): 133-139 -> 133-135
Alt. candidates: [], []                                                                                                           
Model 1BP/2BP comparison:  2BP vs 1BP: 1.18e-07                                                                                   
Rec. model vs L1: 1.78e-07 Rec. model vs L2: 6.04e-297                                                                     
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	133	222.713158	NaN	NaN	NaN	*	*	*
XFG.2	500	133	211.023960	224.588076	-111.176152	8.589243e-06		*
LF.7	58	133	209.386332	220.511282	-103.022563	1.452223e-07		*
XFG.3.1	87	133	204.279382	217.236298	-96.472595	5.491854e-09		*
XFG.1	14	133	154.875852	168.561007	0.877987	3.985062e-30		*
LF.7.3.1	26	133	124.648534	122.184886	93.630229	2.884220e-50		*
LF.7.1.8	44	133	121.420590	118.906272	100.187455	1.085282e-51		*
LF.7.1	165	133	118.390858	127.569470	82.861060	6.290776e-48		*
LF.7.3	54	133	115.594277	113.215491	111.569019	3.667811e-54		*
LF.7.6	15	133	114.046898	111.562751	114.874498	7.044028e-55		*

|||||

XDD.1.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XDD.1.1	29	135	11.897939	NaN	NaN	NaN	*	*	*
JG.3	1482	135	8.733629	-1.266371	20.532743	4.221414e-02	*	*
HK.3	1830	135	7.805379	-2.194621	22.389242	1.665575e-02	*	*
JN.1.3	111	138	6.944593	-17.857062	53.714123	2.633374e-09
XBB.1.5.43	48	137	6.686486	-12.548384	43.096767	5.302061e-07
GK.2.1	255	135	6.461610	-9.629140	37.258280	9.830704e-06		*
BW.1	131	138	5.680314	-13.573433	45.146867	1.902361e-07
XBB.1.16.6	4784	134	5.042190	5.042190	7.915619	2.310387e+01	*	*
XBB.1.16.9	377	138	4.623266	-5.947702	29.895405	3.897520e-04	*
BA.2.76	427	138	4.498727	-14.752670	47.505340	5.845550e-08

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	139	13.542054	None	None	None	*	*	*

Target sequence

, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4822_A|G, 5239_C|T, 6183_A|G, 6351_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 9989_A|G, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 17676_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19273_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21653_T|C, 21711_C|T, 21830_G|A,
21941_G|T, 21987_G|A, 21992_21994, 22016_T|C, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28268_A|C, 28271_A|T, 28297_T|C, 28311_C|T, 28467_A|T,
28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): OZ288088



Target: 530 samples       Number of changes: 138                                           
BC: BA.2.86.1 + XFG.3.1   BC BR: 7-8                    BC BR coord: 3150 - 3151    
Direction L1: <<          Initial region span: 1-7,8-138 Gap history (edge excluded):
Alt. candidates: [], []                                                                           
Model 1BP/2BP comparison: 1BP vs 2BP: 1.17e-04                                                    
Rec. model vs L1: 1.90e-99 Rec. model vs L2: 1.91e-12                                       
Flags: Model_1BP_Best

BA.2.86.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
BA.2.86.1	1343	7	9.416509	NaN	NaN	NaN	*	*	*
JN.1	17255	6	6.528453	4.775698	10.448604	9.657698e-03	*	*
KP.3.1.1	12013	6	6.209902	4.924620	10.150760	1.122064e-02	*	*
XFJ.3	14	3	4.718819	-14.200087	48.400173	5.547992e-11
MC.28.1	17	3	4.718819	-14.200087	48.400173	5.547992e-11
KP.2.14.1	13	3	4.718819	-24.526872	69.053744	1.819891e-15
KP.2.11	40	3	4.718819	-14.200087	48.400173	5.547992e-11
KP.2.10	47	3	4.718819	-14.200087	48.400173	5.547992e-11
KP.1.1.2	12	3	4.718819	-24.179757	68.359513	2.569667e-15
MC.29	54	3	4.718819	-23.971313	67.942626	3.170142e-15

|||||

XFG.3.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3.1	87	8	275.022935	NaN	NaN	NaN	*	*	*
XFG.3	480	8	269.407538	269.407538	-206.815075	3.642810e-03	*	*
LF.7	58	8	263.891557	263.891557	-195.783115	1.459254e-05	*	*
XFG.2	500	8	252.472597	252.472597	-172.945193	1.609383e-10		*
XFG.1	14	8	226.542569	226.542569	-121.085137	8.818679e-22		*
LF.7.3.1	26	14	190.504865	179.848698	-27.697395	4.634711e-42
LF.7.7.1	188	14	186.509746	167.051295	-2.102590	1.279538e-47
LF.7.1	165	14	185.063873	174.428577	-16.857154	2.051855e-44
LF.7.9	20	14	178.128088	167.405781	-2.811562	1.824853e-47
LF.7.1.8	44	14	176.080516	165.463569	1.072861	2.622386e-48

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1784_G|A, 2790_C|T, 3037_C|T, 3140_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4354_G|A, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A,
22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A,
23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28372_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): OZ296928



Target: 530 samples        Number of changes: 154                                               
BC: XEC.2.2.1 + XFG.3      BC BR: 6-7                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-6,9-154 Gap history (edge excluded): 6-9
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  1BP vs 2BP: 1.47e-01                                                        
Rec. model vs L1: 3.27e-226 Rec. model vs L2: 1.04e-07                                           
Flags: Model_1BP_Best

XEC.2.2.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2.2.1	46	6	16.305367	NaN	NaN	NaN	*	*	*
XEC.33	169	6	13.283043	13.283043	-10.566087	4.880122e-02	*	*
KP.2.3.8	103	6	12.992899	12.992899	-9.985799	3.651617e-02	*	*
JN.1	17255	8	11.613198	8.214080	-0.428160	3.065898e-04	*
JN.1.8.1	1498	7	10.262360	9.645172	-3.290343	1.281146e-03	*	*
LF.7.9.3	20	3	7.111420	1.825673	12.348653	5.145362e-07
XFB.3	56	3	6.955858	1.670112	12.659776	4.406566e-07
NY.12.1	17	3	6.912387	-4.824274	25.648547	6.658212e-10
XEL.5	19	3	6.879637	1.593891	12.812218	4.088163e-07
MC.13.2.4	37	3	6.742160	-6.379166	28.758332	1.406144e-10

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	9	317.866398	NaN	NaN	NaN	*	*	*
LF.7	58	9	316.350487	296.350487	-250.700975	2.198082e-01	*	*
XFG.2	500	9	312.830902	285.292272	-228.584545	3.457378e-06		*
XFG.3.1	87	9	284.123042	264.123042	-186.246084	2.222819e-15		*
XFG.1	14	20	267.431167	247.190678	-152.381355	9.820354e-23
LF.7.1	165	20	240.146539	204.660805	-67.321609	3.323402e-41
LF.7.7.1	188	20	225.786977	187.165042	-32.330084	8.386888e-49
LF.7.1.8	44	20	219.625870	184.118082	-26.236163	3.991849e-50
LF.7.6	15	20	212.805087	183.024657	-24.049313	1.335432e-50
LF.7.1.2	26	20	210.437974	174.898264	-7.796528	3.953475e-54

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 533_G|A, 670_T|G, 897_C|A, 1601_C|T, 2500_A|C, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4795_C|T, 5239_C|T, 6183_A|G, 7760_G|A,
7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T,
12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A,
23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24095_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): OZ296975



Target: 530 samples        Number of changes: 156                                                                          
BC: XFG.3 + XDD.1.1 + XFG.3 BC BR: 143-144, 149-150                   BC BR coord: 27915 - 27916, 28880 - 28881      
Direction L1: >>           Initial region span: 1-143,145-149,150-156 Gap history (edge excluded): 143-150 -> 143-145
Alt. candidates: [], []                                                                                                           
Model 1BP/2BP comparison:  2BP vs 1BP: 1.15e-07                                                                                   
Rec. model vs L1: 1.59e-07 Rec. model vs L2: 0.00e+00                                                                      
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	143	290.889872	NaN	NaN	NaN	*	*	*
LF.7	58	143	278.898197	290.023147	-240.046294	5.546104e-07		*
XFG.2	500	143	268.893236	282.457353	-224.914705	2.860084e-10		*
XFG.3.1	87	143	243.743179	256.700095	-173.400191	1.866914e-21		*
XFG.1	14	143	225.223539	238.908693	-137.817386	3.507725e-29		*
LF.7.1	165	143	188.084215	197.262826	-54.525652	2.876285e-47		*
LF.7.6	15	143	185.217225	182.733078	-25.466157	1.407774e-53		*
LF.7.7.1	188	143	182.099682	186.410565	-32.821130	5.553480e-52		*
LF.7.1.8	44	143	177.600079	175.085761	-10.171522	6.701627e-57		*
LF.7.3	54	143	173.829884	171.451098	-2.902196	1.768153e-58		*

|||||

XDD.1.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XDD.1.1	29	145	13.385163	NaN	NaN	NaN	*	*	*
JG.3	1482	145	10.138247	0.138247	17.723506	3.896856e-02	*	*
HK.3	1830	145	9.256169	-0.743831	19.487662	1.608288e-02	*	*
JN.1.3	111	147	8.464940	-16.336019	50.672039	2.727174e-09
XBB.1.5.43	48	147	8.201786	-11.033084	40.066167	5.463533e-07
GK.2.1	255	145	7.855661	-8.235089	34.470179	8.984587e-06		*
BW.1	131	147	7.218843	-12.016026	42.032053	2.050525e-07
XBB.1.16.6	4784	144	6.553074	6.553074	4.893853	2.380748e+01	*	*
BA.2.76	427	147	6.030217	-13.204653	44.409305	6.238132e-08
BA.2.36	3016	147	5.869129	-13.366736	44.733472	5.315785e-08

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	150	13.542054	None	None	None	*	*	*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4822_A|G, 5239_C|T, 6183_A|G, 6351_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 9989_A|G, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19273_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21830_G|A, 21941_G|T, 21987_G|A, 21992_21994, 22016_T|C, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G,
22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A,
22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T,
26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28268_A|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28467_A|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A,
29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): OZ297519



Target: 530 samples       Number of changes: 155                                                       
BC: XFG.3 + KP.3.1.1      BC BR: 135-136                    BC BR coord: 27263 - 27264          
Direction L1: >>          Initial region span: 1-135,137-155 Gap history (edge excluded): 135-137
Alt. candidates: [], []                                                                                       
Model 1BP/2BP comparison: 1BP vs 2BP: 9.14e-03                                                                
Rec. model vs L1: 4.97e-15 Rec. model vs L2: 2.24e-124                                                  
Flags: Model_1BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	135	291.500604	NaN	NaN	NaN	*	*	*
XFG.2	500	135	286.560164	286.560164	-259.120328	7.154598e-03	*	*
LF.7	58	153	281.815826	274.611423	-235.222846	4.621322e-08
XFG.3.1	87	135	239.067128	239.067128	-164.134256	1.689541e-23		*
XFG.1	14	135	223.216992	223.216992	-132.433984	2.209028e-30		*
LF.7.7.1	188	153	205.103504	201.808054	-89.616108	1.117192e-39
LF.7.1	165	135	196.525100	196.525100	-79.050200	5.660849e-42		*
LF.7.1.8	44	135	189.566806	189.566806	-65.133611	5.372693e-45		*
LF.7.6	15	135	181.215978	181.215978	-48.431956	1.270086e-48		*
LF.7.3.1	26	135	174.696536	174.696536	-35.393072	1.871686e-51		*

|||||

KP.3.1.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.1	12013	137	16.044568	NaN	NaN	NaN	*	*	*
JN.1	17255	138	15.166261	-4.833739	59.667477	1.883112e-05	*	*
BA.2.86.1	1343	138	8.957968	-11.042032	72.084064	3.802584e-08		*
NL.11	57	146	8.679461	-27.727278	105.454556	2.157125e-15
FU.1	747	153	6.961561	-43.339202	136.678404	3.567525e-22
MC.24	831	138	6.556822	-13.443178	76.886356	3.432421e-09		*
LF.7	58	138	5.993742	-14.006258	78.012517	1.960630e-09		*
LB.1.3	778	142	3.560375	-22.057930	94.115859	6.225204e-13
JN.1.1	3081	142	3.247294	-22.377540	94.755079	4.520426e-13
XFG.3.1	87	142	2.834986	-22.782033	95.564066	3.030132e-13

Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 1758_C|T, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3569_A|G, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27289_G|T,
27373, 27382_G|C, 27383_A|T, 27384_T|C, 27792_27793, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29682_29683, 29693_T|C

 Case 58 (XFG): OZ297591



Target: 530 samples        Number of changes: 155                                               
BC: BQ.1.10 + XFG.3        BC BR: 8-9                    BC BR coord: 2512 - 2513        
Direction L1: <<           Initial region span: 1-4,9-155 Gap history (edge excluded): 4-9
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 8.48e-07                                           
Flags: Model_2BP_Bad_L1_opp

BQ.1.10 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
BQ.1.10	2048	4	6.071544	NaN	NaN	NaN	*	*	*
JN.11	67	3	5.085550	-31.287095	88.574190	2.318339e-10		*
KP.2.3.10	10	3	4.790433	-31.582212	89.164424	1.726077e-10		*
DN.3	10	3	4.685073	-48.767248	123.534496	5.938946e-18		*
BF.5.5	91	3	4.661600	-48.338270	122.676541	9.084155e-18		*
PL.1.1	12	3	4.608112	-31.764534	89.529067	1.434550e-10		*
BA.2.75.2	753	4	4.491154	-11.625361	49.250722	8.005831e-02	*	*
BN.1.1.1	41	3	4.453366	-45.546634	117.093268	1.486407e-16		*
CM.4	76	3	4.148579	-58.425110	142.850219	3.788128e-22		*
PD.2	21	3	4.048496	-38.934158	103.868317	1.103632e-13		*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	9	297.369129	NaN	NaN	NaN	*	*	*
XFG.2	500	8	292.061966	291.675165	-241.350330	3.362737e-03	*	*
LF.7	58	9	281.650636	281.650636	-221.301272	1.488986e-07		*
XFG.3.1	87	9	249.645042	249.645042	-157.290084	1.876272e-21		*
XFG.1	14	9	232.798710	232.798710	-123.597419	9.069959e-29		*
LF.7.7.1	188	15	194.306068	184.863763	-27.727526	1.379429e-49
LF.7.1	165	15	190.644805	190.020322	-38.040643	2.390492e-47
LF.7.1.8	44	15	183.800033	183.193899	-24.387797	2.596734e-50
LF.7.1.2	26	15	169.255147	168.570572	4.858856	1.155768e-56
LF.7.6	15	15	168.565878	167.959744	6.080511	6.279876e-57

Target sequence

, 241_C|T, 670_T|G, 683_C|T, 684_T|C, 897_C|A, 1263_C|T, 2334_C|T, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11173_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T,
12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18828_C|T, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T,
21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G,
22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A,
22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A,
23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|A, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 27942_C|T, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A,
29409_C|T, 29510_A|C, 29645_G|T

 Case 58 (XFG): USA/CA-CDPH-500147587/2025



Target: 530 samples        Number of changes: 152                                           
BC: FL.29 + XFG.3          BC BR: 3-4                    BC BR coord: 1960 - 1961    
Direction L1: <<           Initial region span: 1-3,4-152 Gap history (edge excluded):
Alt. candidates: [], []                                                                            
Model 1BP/2BP comparison:  -                                                                       
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 1.09e-14                                       
Flags: Model_2BP_Bad_L1_opp

FL.29 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
FL.29	37	3	4.711568	NaN	NaN	NaN	*	*	*
DS.3	91	3	4.062575	4.062575	1.874850	0.524663	*	*
JN.1.42.1	18	3	4.058777	4.058777	1.882447	0.522046	*	*
BA.2.86	38	3	3.073585	3.073585	3.852830	0.194952	*	*
BA.5.1.30	4775	3	3.037057	3.037057	3.925885	0.187308	*	*
BA.5.1.12	592	3	2.876304	2.876304	4.247392	0.159614	*	*
HN.8	13	3	2.813097	2.813097	4.373805	0.150318	*	*
BN.1.5	1025	3	2.731778	2.731778	4.536444	0.138069	*	*
BN.1.3.1	1042	3	2.308064	2.308064	5.383873	0.090718	*	*
BA.2.75.2	753	3	1.944050	1.944050	6.111900	0.062976	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	4	284.794795	NaN	NaN	NaN	*	*	*
XFG.2	500	4	266.630867	259.092237	-170.184474	6.862152e-12		*
LF.7	58	4	259.956453	259.956453	-171.912907	1.629765e-11		*
XFG.3.1	87	4	255.385880	255.385880	-162.771760	1.688104e-13		*
XFG.1	14	4	224.571728	224.571728	-101.143455	6.992216e-27		*
LF.7.7.1	188	10	192.035626	182.593321	-17.186642	4.121962e-45
LF.7.1	165	10	191.785480	191.160997	-34.321995	2.161903e-41
LF.7.1.8	44	33	172.591950	163.169373	21.661254	1.509849e-53
LF.7.6	15	33	163.576197	159.880978	28.238044	5.624770e-55
LF.7.1.2	26	33	162.505401	153.050903	41.898195	6.079579e-58

Target sequence

, 241_C|T, 670_T|G, 1960_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6286_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10156_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11681_C|T, 11727_G|A, 12469_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24328_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26058_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29249_C|T, 29409_C|T, 29510_A|C

 Case 58 (XFG): USA/CA-GBW-GKISBBBE69940/2025



Target: 530 samples       Number of changes: 151                                                      
BC: LF.7 + NL.11 + LF.7   BC BR: 4-5, 7-8                   BC BR coord: 672 - 673, 2789 - 2790
Direction L1: <<          Initial region span: 1-4,5-7,8-151 Gap history (edge excluded): 4-8 ->
Alt. candidates: [], []                                                                                      
Model 1BP/2BP comparison: 2BP vs 1BP: 2.08e-05                                                               
Rec. model vs L1: 1.27e-14 Rec. model vs L2: 6.30e-205                                                 
Flags: Model_2BP_Best

LF.7 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	4	6.259952	None	None	None	*	*	*

|||||

NL.11 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
NL.11	57	5	9.486351	NaN	NaN	NaN	*	*	*
JN.1.42.2	28	6	8.220027	-1.779973	9.559946	1.281364e-05	*	*
MC.10.1.7	11	6	8.092091	-1.907909	9.815817	1.125160e-05	*	*
JN.1.15.1	15	6	7.712944	-2.287056	10.574113	7.733106e-06		*
JN.1.13	24	6	7.269373	-2.730627	11.461253	4.955562e-06		*
MH.1	51	6	7.169630	-2.830370	11.660739	4.483978e-06		*
BA.2.26	600	7	6.860964	-13.139036	32.278072	1.493095e-10
MC.13.1	123	6	6.760021	-3.239979	12.479958	2.975793e-06		*
MC.1.2	49	6	6.598166	-3.401834	12.803667	2.535804e-06		*
KP.2.8	51	6	6.558161	-3.441839	12.883678	2.436373e-06		*

|||||

LF.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	8	339.385844	NaN	NaN	NaN	*	*	*
XFG.3	480	8	338.775564	344.799659	-347.599318	4.295574e-01	*	*
XFG.2	500	8	332.375070	336.310896	-330.621791	8.827973e-05	*	*
XFG.3.1	87	8	303.976289	309.017670	-276.035339	1.241551e-16		*
XFG.1	14	8	275.682307	280.040099	-218.080198	3.221889e-29		*
LF.7.1	165	14	247.879235	252.484203	-162.968406	3.476371e-41
LF.7.7.1	188	14	239.084093	233.933701	-125.867402	3.054664e-49
LF.7.1.8	44	14	226.485303	229.533144	-117.066289	3.750315e-51
LF.7.1.2	26	14	220.581658	224.626234	-107.252468	2.764915e-53
PC.3	42	14	218.363457	221.932793	-101.865586	1.876850e-54

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2003_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 13427_G|A, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A,
23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/CA-LACPHL-AY12256/2025



Target: 530 samples        Number of changes: 150                                           
BC: JN.11 + XFG.2          BC BR: 4-5                    BC BR coord: 2067 - 2068    
Direction L1: <<           Initial region span: 1-4,5-150 Gap history (edge excluded):
Alt. candidates: [], []                                                                            
Model 1BP/2BP comparison:  -                                                                       
Rec. model vs L1: 5.51e-229 Rec. model vs L2: 8.32e-17                                       
Flags: Model_2BP_Bad_L1_opp

JN.11 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.11	67	4	8.712905	NaN	NaN	NaN	*	*	*
KP.2.3.10	10	4	8.417788	8.417788	-2.835576	0.744532	*	*
PL.1.1	12	4	8.235466	8.235466	-2.470933	0.618783	*	*
PD.2	21	4	7.675851	1.065842	11.868317	0.000476	*	*
KP.4.2.4	22	4	7.629331	-0.408730	14.817461	0.000109	*	*
KR.1.4	24	4	7.408788	0.164265	13.671469	0.000194	*	*
KP.3.1.2	28	4	7.277693	7.277693	-0.555386	0.238115	*	*
JN.1.69	32	4	7.254637	7.254637	-0.509274	0.232236	*	*
JN.1.50.2	33	4	7.162322	7.162322	-0.324644	0.211189	*	*
LP.8.1.10	32	4	7.156197	0.546188	12.907624	0.000283	*	*

|||||

XFG.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.2	500	5	328.815526	NaN	NaN	NaN	*	*	*
XFG.3	480	1	327.929777	323.397837	-308.795673	4.449338e-03	*
LF.7	58	4	316.567111	312.939756	-287.879512	1.275191e-07		*
XFG.3.1	87	4	284.800151	281.172796	-224.345592	2.042730e-21		*
XFG.1	14	4	269.199060	265.571706	-193.143411	3.412287e-28		*
LF.7.1	165	1	238.824969	232.547938	-127.095876	1.558266e-42
LF.7.1.8	44	4	207.698916	204.118082	-70.236163	7.008895e-55		*
LF.7.7.1	188	11	202.783973	193.341668	-48.683335	1.458663e-59
LF.7.2.1	67	4	193.721203	190.124154	-42.248307	5.857311e-61		*
LF.7.6	15	4	192.551537	188.924182	-39.848364	1.764188e-61		*

Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T,
9344_C|T, 9370_T|C, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14407_C|T,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 16887_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T,
25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759, 29762_C|T

 Case 58 (XFG): USA/CA-LACPHL-AY12331/2025



Target: 530 samples        Number of changes: 157                                                 
BC: JN.1.39.1 + XFG.3      BC BR: 7-8                     BC BR coord: 896 - 897           
Direction L1: <<           Initial region span: 1-4,12-157 Gap history (edge excluded): 4-12
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  -                                                                             
Rec. model vs L1: 3.55e-208 Rec. model vs L2: 1.32e-08                                             
Flags: Model_2BP_Bad_L1_opp

JN.1.39.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.39.1	40	4	10.004107	NaN	NaN	NaN	*	*	*
KP.2.3	4440	11	8.183088	6.529182	0.941637	6.110447	*
KP.3.1.1	12013	10	8.044589	7.668120	-1.336240	19.105954	*
MC.1.4	125	4	8.028188	2.742441	8.515117	0.138069	*	*
JN.1.65.1	46	4	7.964333	2.656608	8.686784	0.126818	*	*
KP.4	35	4	7.765644	2.479897	9.040205	0.106459	*	*
MC.29	54	4	7.024352	1.738605	10.522790	0.050793	*	*
LP.8.1.1	2345	7	6.709351	6.709351	0.581298	7.315534	*
JN.9	55	4	6.041964	0.737868	12.524264	0.018686	*	*
NY.7.1	28	4	5.870125	0.548011	12.903978	0.015452	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	12	283.953713	NaN	NaN	NaN	*	*	*
LF.7	58	12	281.314074	262.377777	-176.755553	7.100535e-02	*	*
XFG.2	500	9	271.587245	263.886152	-179.772304	3.198190e-01	*
XFG.3.1	87	12	261.076804	242.157898	-136.315796	1.174510e-10		*
XFG.1	14	12	246.130355	227.211449	-106.422899	3.777062e-17		*
LF.7.7.1	188	18	205.103639	179.552840	-11.105679	7.600648e-38
LF.7.1	165	18	203.360460	184.752458	-21.504917	1.370915e-35
LF.7.1.8	44	18	194.998404	165.462551	17.074897	5.776189e-44
LF.7.6	15	18	191.770351	162.234498	23.531003	2.284916e-45
LF.7.3	54	18	188.534008	158.922305	30.155390	8.302024e-47

Target sequence

, 21_C|T, 44_C|T, 174_G|T, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3049_T|C, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G,
7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T,
12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16173_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28473_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29137_C|T, 29367_C|T,
29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/CA-LACPHL-AY12367/2025



Target: 530 samples        Number of changes: 156                                                                          
BC: XFG.3 + BA.2.38 + XFG.3 BC BR: 145-146, 150-151                   BC BR coord: 28361 - 28362, 28883 - 28884      
Direction L1: >>           Initial region span: 1-145,146-150,154-156 Gap history (edge excluded): 145-154 -> 150-154
Alt. candidates: [], []                                                                                                           
Model 1BP/2BP comparison:  2BP vs 1BP: 2.19e-05                                                                                   
Rec. model vs L1: 4.09e-13 Rec. model vs L2: 0.00e+00                                                                      
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	145	266.186454	NaN	NaN	NaN	*	*	*
LF.7	58	145	265.971646	255.442099	-166.884199	7.171897e-02	*	*
XFG.2	500	145	259.041385	250.951004	-157.902009	8.047330e-04	*	*
XFG.3.1	87	145	243.919801	235.222221	-126.444442	1.186314e-10		*
XFG.1	14	145	228.245114	220.275772	-96.551544	3.834145e-17		*
LF.7.1	165	145	201.087613	188.629965	-33.259930	6.924999e-31		*
LF.7.6	15	145	186.244100	162.105457	19.789086	2.092949e-42		*
LF.7.7.1	188	145	184.706097	167.362483	9.275033	4.008446e-40		*
LF.7.1.8	44	145	182.626179	158.457365	27.085271	5.439810e-44		*
LF.7.3	54	145	176.001218	151.967935	40.064129	8.302024e-47		*

|||||

BA.2.38 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
BA.2.38	911	150	9.861020	NaN	NaN	NaN	*	*	*
XBB.1.42	71	146	7.808425	-0.537078	15.074157	3.058503e-05	*
XBB.1.5.33	820	150	6.914078	6.914078	0.171844	5.260206e-02	*	*
JD.1	35	146	6.723997	-1.621506	17.243012	1.033474e-05	*
HN.3.1	55	146	6.272012	-2.073491	18.146982	6.556852e-06
AD.2	3211	146	6.011670	-2.336637	18.673275	5.055671e-06
XBB.1.5.85	30	146	5.779536	-2.565968	19.131935	4.016900e-06
AY.109	471	146	5.075648	-35.961016	85.922033	1.260744e-20
JN.1.32	436	146	5.049001	-3.296502	20.593005	1.935780e-06
MC.23	64	146	5.021850	-3.323653	20.647307	1.878569e-06

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	154	8.279257	None	None	None	*	*	*

Target sequence

, 174_G|T, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16173_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20235_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A,
23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28473_C|A, 28817_G|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29137_C|T, 29367_C|T,
29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/CA-LACPHL-AY12442/2025



Target: 530 samples        Number of changes: 153                                                 
BC: KP.3.1.1 + XFG.3       BC BR: 10-11                   BC BR coord: 3773 - 3774         
Direction L1: <<           Initial region span: 1-9,11-153 Gap history (edge excluded): 9-11
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  1BP vs 2BP: 1.37e-05                                                          
Rec. model vs L1: 1.73e-128 Rec. model vs L2: 9.81e-15                                             
Flags: Model_1BP_Best

KP.3.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.1	12013	9	13.231814	NaN	NaN	NaN	*	*	*
JN.1	17255	9	12.499233	9.829579	6.340841	8.374323e-02	*	*
JN.1.65	124	9	9.792360	-0.207640	26.415280	3.652860e-06		*
JN.1.11.1	226	4	9.089588	-2.624465	31.248930	3.264464e-07
KP.1.1	593	4	8.164083	-3.549315	33.098629	1.294463e-07
MC.42	84	9	7.714779	-2.285221	30.570442	4.586401e-07		*
LP.8.1.1	2345	4	6.795103	0.039528	25.920945	4.690366e-06
JN.1.8.1	1498	9	5.526092	-4.473908	34.947815	5.132951e-08		*
LF.7.3.5	16	3	4.718819	-16.963892	59.927783	1.932098e-13
LD.2	13	3	4.718819	-31.985883	89.971766	5.793299e-20

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	11	268.953360	NaN	NaN	NaN	*	*	*
XFG.1	14	11	258.818365	258.818365	-185.636729	3.966664e-05	*	*
LF.7	58	11	253.575487	253.575487	-175.150973	2.091948e-07		*
XFG.2	500	11	242.250753	242.250753	-152.501507	2.524445e-12		*
XFG.3.1	87	11	234.418810	234.418810	-136.837620	1.003784e-15		*
LF.7.7.1	188	13	189.730052	171.975791	-11.951581	7.622916e-43
LF.7.1	165	13	185.651765	176.728342	-21.456685	8.855058e-41
LF.7.1.2	26	13	170.026899	161.103475	9.793049	1.449907e-47
LF.7.1.8	44	13	165.758332	156.834909	18.330182	2.027228e-49
LF.7.6	15	13	162.464213	153.540790	24.918419	7.514539e-51

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1169_T|C, 2344_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3773_C|T, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16224_T|C, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20134_G|T, 20320_C|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22595_A|T, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G,
22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23371_T|C, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29200_C|T, 29409_C|T, 29510_A|C, 29651_G|T, 29734_29759

 Case 58 (XFG): USA/CA-LACPHL-AY12607/2025



Target: 530 samples        Number of changes: 153                                               
BC: KP.2.3.10 + LF.7       BC BR: 5-6                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-5,7-153 Gap history (edge excluded): 5-7
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  1BP vs 2BP: 4.89e-01                                                        
Rec. model vs L1: 4.17e-212 Rec. model vs L2: 5.56e-08                                           
Flags: Model_1BP_Best

KP.2.3.10 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3.10	10	5	10.375656	NaN	NaN	NaN	*	*	*
JN.11	67	5	10.021428	10.021428	-10.042857	0.701173	*	*
KP.4.2.4	22	5	9.715032	9.715032	-9.430064	0.516851	*	*
PL.1.1	12	5	9.317865	9.317865	-8.635731	0.348192	*	*
XEC.2.2.1	46	5	9.173366	9.173366	-8.346733	0.301194	*	*
KR.1.4	24	5	9.050803	9.050803	-8.101605	0.265803	*	*
MK.1	151	5	8.914620	8.914620	-7.829239	0.232236	*	*
JN.1.69	32	5	8.860284	8.860284	-7.720569	0.219808	*	*
KP.3.1.2	28	5	8.765557	8.765557	-7.531114	0.199888	*	*
LB.1.4.1	74	5	8.648070	8.648070	-7.296139	0.178173	*	*

|||||

LF.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	7	305.098200	NaN	NaN	NaN	*	*	*
XFG.2	500	6	299.104506	291.565876	-241.131752	2.915876e-02	*	*
XFG.3	480	7	293.171216	283.171216	-224.342433	6.589718e-06		*
XFG.3.1	87	7	259.640359	249.640359	-157.280718	1.807061e-20		*
XFG.1	14	18	257.861264	247.620775	-153.241550	2.397165e-21
LF.7.1	165	23	223.177472	202.427688	-62.855377	5.674536e-41
LF.7.1.8	44	23	216.438824	184.118082	-26.236163	6.338674e-49
LF.7.7.1	188	23	208.776556	184.706634	-27.413269	1.137786e-48
LF.7.6	15	23	195.517566	168.924182	4.151636	1.595489e-55
LF.7.1.2	26	23	194.393647	162.040983	17.918034	1.632211e-58

Target sequence

, 44_C|T, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4222_A|G, 4321_C|T, 5239_C|T, 6183_A|G, 6312_C|T, 7842_A|G, 7869_C|T,
8293_C|T, 8326_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 18981_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/CA-LACPHL-AY12732/2025



Target: 530 samples        Number of changes: 159                                                       
BC: XFG.2 + BE.5           BC BR: 153-154                    BC BR coord: 28958 - 28959          
Direction L1: >>           Initial region span: 1-148,156-159 Gap history (edge excluded): 148-156
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 5.62e-14 Rec. model vs L2: 0.00e+00                                                   
Flags: Model_2BP_Bad_L1_opp

XFG.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.2	500	148	253.255377	NaN	NaN	NaN	*	*	*
XFG.3	480	148	248.327684	243.590481	-139.180962	7.226503e-03	*	*
LF.7	58	148	247.650734	242.913531	-137.827062	3.679421e-03	*	*
XFG.3.1	87	148	225.352179	220.614975	-93.229951	7.603481e-13		*
XFG.1	14	148	208.014349	203.277146	-58.554292	2.240506e-20		*
LF.7.1	165	148	181.692471	176.937031	-5.874061	8.147597e-32		*
LF.7.6	15	148	167.383881	162.646678	22.706644	5.069456e-38		*
LF.7.7.1	188	148	164.543438	159.806235	28.387530	2.961863e-39		*
LF.7.1.8	44	148	161.921450	157.184246	33.631507	2.156321e-40		*
LF.7.3	54	148	155.754705	151.017502	45.964997	4.531980e-43		*

|||||

BE.5 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
BE.5	231	156	7.549258	NaN	NaN	NaN	*	*	*
BF.38	60	157	7.093101	-22.906899	59.813797	2.880389e-05	*	*
BQ.1.1.5	1362	157	7.023821	-13.289818	40.579637	4.317105e-01	*	*
FY.6	11	157	6.947943	-23.052057	60.104113	2.491601e-05	*	*
JN.1.1	3081	150	6.733092	1.471920	11.056161	1.110144e+06	*
PG.3	31	157	6.524418	-29.673996	73.347993	3.305807e-08		*
FY.3.3	33	157	6.508577	-23.491423	60.982846	1.604682e-05	*	*
BQ.1.1.74	24	157	6.486239	-23.513761	61.027523	1.565062e-05	*	*
XBB.1.5.25	43	157	6.222814	-23.777186	61.554373	1.206744e-05	*	*
XEC.2	921	156	6.120054	-4.495483	22.990967	2.849788e+03	*	*

Target sequence

, 21_C|T, 44_C|T, 174_G|T, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 7842_A|G,
7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 14895_T|C, 15714_C|T, 15756_T|A, 16173_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20235_C|T, 21411_C|T, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28473_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29137_C|T, 29367_C|T,
29409_C|T, 29510_A|C, 29543_G|C, 29734_29759

 Case 58 (XFG): USA/CA-LACPHL-AY12742/2025



Target: 530 samples       Number of changes: 151                                                          
BC: XFG.3 + JJ.1 + XFG.3  BC BR: 5-6, 8-9                   BC BR coord: 2335 - 2336, 3430 - 3431  
Direction L1: <<          Initial region span: 1-4,6-8,9-151 Gap history (edge excluded): 4-9 -> 4-6
Alt. candidates: [], []                                                                                          
Model 1BP/2BP comparison: 2BP vs 1BP: 1.47e-02                                                                   
Rec. model vs L1: 1.19e-08 Rec. model vs L2: 0.00e+00                                                      
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	4	6.540343	None	None	None	*	*	*

|||||

JJ.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JJ.1	58	6	9.078968	NaN	NaN	NaN	*	*	*
JN.2.3	36	6	6.260055	6.260055	-4.520111	5.960594e-02	*	*
XBB.1.5.3	150	6	5.526086	5.526086	-3.052172	2.858137e-02	*	*
KP.2.3.5	89	6	5.354938	5.354938	-2.709876	2.411310e-02	*	*
XEC.8	592	6	5.251827	5.251827	-2.503654	2.170962e-02	*	*
B.1.260	81	8	5.061178	-5.066705	18.133410	7.192909e-07
B.1.1.70	669	7	4.898144	-5.101856	18.203713	6.945512e-07		*
XBB.1.5.14	241	6	4.354619	-2.070485	12.140970	1.437529e-05	*	*
MC.24	831	6	4.217147	4.217147	-0.434294	7.711828e-03	*	*
BA.5.9	2618	6	4.166044	4.166044	-0.332088	7.335718e-03	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	9	315.853318	NaN	NaN	NaN	*	*	*
LF.7	58	9	311.671369	308.339398	-272.678795	1.733548e-02	*	*
XFG.2	500	9	300.299960	295.867638	-247.735275	6.657079e-08		*
XFG.3.1	87	18	293.143640	289.059389	-234.118778	7.340713e-11
XFG.1	14	18	277.431167	271.756651	-199.513302	2.240125e-18
LF.7.1	165	18	239.522535	219.125767	-94.251533	3.114251e-41
LF.7.7.1	188	18	235.786977	211.782230	-79.564460	2.011225e-44
LF.7.6	15	18	222.805087	208.437928	-72.875856	7.127170e-46
LF.7.1.2	26	18	220.437974	199.761489	-55.522978	1.211270e-49
LF.7.3	54	18	219.568744	204.413895	-64.827790	1.273157e-47

Target sequence

, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1784_G|A, 2790_C|T, 3037_C|T, 3095_T|C, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4354_G|A, 5239_C|T, 6183_A|G, 7777_C|T, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28372_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/CA-LACPHL-AY12924/2025



Target: 530 samples        Number of changes: 155                                                 
BC: JN.11 + LF.7           BC BR: 8-9                     BC BR coord: 2792 - 2793         
Direction L1: <<           Initial region span: 1-4,13-155 Gap history (edge excluded): 4-13
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  -                                                                             
Rec. model vs L1: 7.59e-229 Rec. model vs L2: 4.10e-08                                             
Flags: Model_2BP_Bad_L1_opp

JN.11 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.11	67	4	8.712905	NaN	NaN	NaN	*	*	*
LP.8.1	1124	5	8.478730	-7.425220	36.850441	356824.734345	*	*
KP.2.3.10	10	4	8.417788	-20.505004	63.010008	0.744532	*	*
PL.1.1	12	4	8.235466	-20.687326	63.374651	0.621885	*	*
PD.2	21	4	7.675851	-27.856950	77.713901	0.000478	*	*
KP.4.2.4	22	4	7.629331	-29.331522	80.663045	0.000109	*	*
KR.1.4	24	4	7.408788	-28.758527	79.517053	0.000194	*	*
KP.3.1.2	28	4	7.277693	-21.645099	65.290198	0.238115	*	*
JN.1.69	32	4	7.254637	-21.668155	65.336310	0.232236	*	*
JN.1.50.2	33	4	7.162322	-21.760470	65.520940	0.212248	*	*

|||||

LF.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	13	296.767482	NaN	NaN	NaN	*	*	*
XFG.3	480	13	284.946380	282.104480	-226.208959	7.138556e-06		*
XFG.2	500	13	280.776755	278.012828	-218.025655	1.194940e-07		*
XFG.3.1	87	13	251.484913	248.563151	-159.126302	1.938088e-20		*
XFG.1	14	13	235.397068	232.637149	-127.274299	2.339173e-27		*
LF.7.1	165	15	201.503267	189.801576	-41.603152	5.835233e-46
LF.7.1.8	44	15	194.724215	183.040874	-28.081747	6.764373e-49
LF.7.7.1	188	15	192.783973	172.264460	-6.528919	1.414831e-53
LF.7.6	15	15	179.530316	167.846974	2.306052	1.702640e-55
LF.7.3	54	15	176.188613	164.429420	9.141160	5.597669e-57

Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 1238_C|T, 1844_A|C, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3569_A|G, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27630_C|T, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29422_G|A, 29510_A|C, 29682_29683, 29693_T|C,
29734_29759

 Case 58 (XFG): USA/CA-LACPHL-AY13064/2025



Target: 530 samples        Number of changes: 155                                                   
BC: KP.3.1.1 + XFG.3       BC BR: 11-12                    BC BR coord: 3773 - 3774          
Direction L1: <<           Initial region span: 1-10,12-155 Gap history (edge excluded): 10-12
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  1BP vs 2BP: 1.76e-05                                                            
Rec. model vs L1: 9.76e-129 Rec. model vs L2: 1.27e-14                                               
Flags: Model_1BP_Best

KP.3.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.1	12013	10	14.815722	NaN	NaN	NaN	*	*	*
JN.1	17255	10	13.427482	10.757828	12.484345	4.349975e-02	*	*
JN.1.65	124	10	10.554287	0.554287	32.891426	1.608835e-06		*
JN.1.11.1	226	5	10.475037	-1.239016	36.478032	2.672717e-07
KP.1.1	593	5	9.615892	-2.097506	38.195012	1.130993e-07
MC.42	84	10	8.930710	-1.069290	36.138581	3.167985e-07		*
LP.8.1.1	2345	5	8.231787	1.476211	31.047579	4.037035e-06
XEC.35.1	28	4	7.305296	-20.777145	75.554290	8.770216e-16
LF.7.1.11	20	4	7.236303	-27.355280	88.710561	1.217174e-18
NC.1.2.1	10	4	7.236303	-31.841643	97.683285	1.372593e-20

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	12	273.648542	NaN	NaN	NaN	*	*	*
XFG.1	14	12	262.294685	262.294685	-188.589370	1.171079e-05	*	*
LF.7	58	12	257.422181	257.422181	-178.844361	8.941298e-08		*
XFG.2	500	12	246.001670	246.001670	-156.003341	9.812001e-13		*
XFG.3.1	87	12	238.901493	238.901493	-141.802986	8.095930e-16		*
LF.7.7.1	188	14	193.553426	175.799165	-15.598331	3.193633e-43
LF.7.1	165	14	189.433786	180.510363	-25.020726	3.546598e-41
LF.7.1.2	26	14	172.884180	163.960757	8.078487	2.302705e-48
LF.7.6	15	14	166.564688	157.641265	20.717470	4.144739e-51
LF.7.3	54	14	163.328345	154.386230	27.227540	1.599074e-52

Target sequence

, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1169_T|C, 2344_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3773_C|T, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16224_T|C, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20134_G|T, 20320_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22595_A|T, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A,
23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23371_T|C, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29200_C|T, 29409_C|T, 29510_A|C,
29651_G|T, 29734_29759

 Case 58 (XFG): USA/CA-LACPHL-AY13080/2025



Target: 530 samples            Number of changes: 155                                                      
BC: XFG.3 + XBB.1.16.22 + XFG.3 BC BR: 4-5, 8-9                   BC BR coord: 896 - 897, 3176 - 3177
Direction L1: <<               Initial region span: 1-4,5-8,9-155 Gap history (edge excluded): 4-9 ->
Alt. candidates: [], []                                                                                           
Model 1BP/2BP comparison:      2BP vs 1BP: 3.02e-10                                                               
Rec. model vs L1: 3.56e-15     Rec. model vs L2: 0.00e+00                                                  
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	4	4.53194	None	None	None	*	*	*

|||||

XBB.1.16.22 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XBB.1.16.22	25	8	8.182764	NaN	NaN	NaN	*	*	*
GN.1.1	93	8	7.347076	7.347076	-4.694153	4.317105e-01	*	*
AY.73	462	5	5.908262	-14.087852	38.175704	2.118802e-10
AY.71	260	5	5.908262	-0.407936	10.815872	1.850286e-04	*
AY.72	300	5	5.908262	-14.087852	38.175704	2.118802e-10
B.1.1.181	17	5	5.908262	-14.087852	38.175704	2.118802e-10
AY.2	1597	5	5.907009	-21.536087	53.072174	1.238135e-13
AY.38	560	5	5.897490	-14.098624	38.197248	2.097720e-10
AY.74	544	5	5.897171	-3.465409	16.930818	8.719052e-06
AY.29.2	32	5	5.843723	-14.152391	38.304781	1.995413e-10

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	9	294.248491	NaN	NaN	NaN	*	*	*
LF.7	58	9	285.286785	280.005604	-214.011208	7.016509e-09		*
XFG.2	500	9	281.759859	276.448478	-206.896956	2.005415e-10		*
XFG.3.1	87	9	253.041948	247.760767	-149.521534	6.954974e-23		*
XFG.1	14	9	236.109583	230.828403	-115.656805	3.088090e-30		*
LF.7.1	165	15	204.215007	199.856741	-53.713482	1.089980e-43
LF.7.7.1	188	15	195.542400	181.508428	-17.016856	1.175672e-51
LF.7.1.8	44	15	183.653934	167.686297	10.627406	1.164568e-57
LF.7.6	15	15	182.560510	166.662382	12.675236	4.178429e-58
LF.7.3	54	15	179.324167	163.331496	19.337008	1.495590e-59

Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2509_C|T, 2790_C|T, 3037_C|T, 3176_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5184_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16329_C|T, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 18981_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 20679_G|T,
21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G,
22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22525_A|G, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T,
26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A,
29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/CA-LACPHL-AY13088/2025



Target: 530 samples        Number of changes: 155                                               
BC: BA.2.76 + XFG.3        BC BR: 4-5                    BC BR coord: 672 - 673          
Direction L1: <<           Initial region span: 1-4,7-155 Gap history (edge excluded): 4-7
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 2.63e-13                                           
Flags: Model_2BP_Bad_L1_opp

BA.2.76 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
BA.2.76	427	4	4.529835	NaN	NaN	NaN	*	*	*
KP.3.1.1	12013	5	3.256950	-0.356743	8.713486	0.007559	*	*
BF.14	1581	4	3.190337	3.190337	1.619326	0.261846	*	*
KP.2.3	4440	6	2.973530	-0.854327	9.708655	0.004585	*
BQ.1.1.10	705	4	2.831446	2.831446	2.337108	0.182684	*	*
LP.8.1.1	2345	5	2.630623	-0.968622	9.937244	0.004087	*	*
B.1.349	537	3	1.593554	-8.406446	24.812891	0.000002		*
B.1.1.7	477665	3	1.434268	-8.565732	25.131465	0.000002		*
BE.1.1.2	2143	4	1.170904	1.170904	5.658191	0.034735	*	*
BA.5	6418	4	0.522220	0.522220	6.955560	0.018133	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	7	276.923940	NaN	NaN	NaN	*	*	*
LF.7	58	7	272.735071	266.362426	-180.724851	1.529851e-02	*	*
XFG.2	500	7	261.371004	257.283167	-162.566334	1.751567e-06		*
XFG.3.1	87	7	254.123042	247.750397	-143.500793	1.265986e-10		*
XFG.1	14	7	237.190678	230.818032	-109.636065	5.621124e-18		*
LF.7.7.1	188	15	195.542400	170.754452	10.491096	4.612380e-44
LF.7.1	165	15	193.591003	188.598160	-25.196321	2.593643e-36
LF.7.6	15	15	182.560510	166.652011	18.695977	7.605824e-46
LF.7.3	54	15	179.324167	163.339818	25.320364	2.777356e-47
LF.7.1.2	26	15	174.512558	158.486398	35.027204	2.163375e-49

Target sequence

, 174_G|T, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16173_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20235_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A,
23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28473_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29137_C|T, 29367_C|T, 29409_C|T,
29510_A|C, 29734_29759

 Case 58 (XFG): USA/CA-LACPHL-AY13108/2025



Target: 530 samples        Number of changes: 156                                                   
BC: KP.2 + XFG.3           BC BR: 11-12                    BC BR coord: 4188 - 4189          
Direction L1: <<           Initial region span: 1-11,18-156 Gap history (edge excluded): 11-18
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 3.83e-111 Rec. model vs L2: 6.48e-19                                               
Flags: Model_2BP_Bad_L1_opp

KP.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2	1589	11	19.833322	NaN	NaN	NaN	*	*	*
KP.2.3	4440	11	14.388256	14.388256	-0.776512	4.317840e-03	*	*
MC.1	932	9	14.268497	5.345074	17.309852	5.094164e-07
KP.3.1.4	511	9	14.077741	5.154318	17.691364	4.212666e-07
KP.3.1.1	12013	9	12.914215	3.990376	20.019249	1.314026e-07
JN.1	17255	11	12.855362	12.855362	2.289275	9.303032e-04	*	*
KP.2.2	1334	9	12.162400	3.238977	21.522046	6.207019e-08
JN.1.7	1974	9	11.375845	2.451915	23.096170	2.817023e-08
JN.1.4.5	1757	9	9.356603	0.433180	27.133640	3.755667e-09
LD.1	70	4	9.085704	-20.263175	68.526350	3.844070e-18

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	18	244.192233	NaN	NaN	NaN	*	*	*
LF.7	58	18	242.885348	239.565012	-145.130025	3.456202e-02	*	*
XFG.2	500	18	234.896342	228.240279	-122.480558	4.170749e-07		*
XFG.3.1	87	18	228.660957	220.408336	-106.816672	1.658396e-10		*
XFG.1	14	18	213.954846	204.320491	-74.640982	1.705651e-17		*
LF.7.1	165	18	175.740514	150.879263	32.241474	1.054855e-40		*
LF.7.7.1	188	18	171.963602	152.783973	28.432055	7.088004e-40		*
LF.7.1.8	44	18	167.680110	142.778456	48.443088	3.201899e-44		*
LF.7.6	15	18	158.704612	139.530316	54.939368	1.241511e-45		*
LF.7.1.2	26	18	157.580693	132.725558	68.548884	1.375868e-48		*

Target sequence

, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3951_3953, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 6268_C|T, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16173_C|T, 16600_T|C, 17410_C|T, 18048_T|C, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22082_C|T, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A,
23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28473_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29137_C|T, 29367_C|T, 29409_C|T,
29510_A|C, 29734_29759

 Case 58 (XFG): USA/CA-LACPHL-AY13110/2025



Target: 530 samples        Number of changes: 155                                               
BC: BA.2.76 + XFG.3        BC BR: 4-5                    BC BR coord: 672 - 673          
Direction L1: <<           Initial region span: 1-4,7-155 Gap history (edge excluded): 4-7
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 2.63e-13                                           
Flags: Model_2BP_Bad_L1_opp

BA.2.76 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
BA.2.76	427	4	4.529835	NaN	NaN	NaN	*	*	*
KP.3.1.1	12013	5	3.256950	-0.356743	8.713486	0.007559	*	*
BF.14	1581	4	3.190337	3.190337	1.619326	0.261846	*	*
KP.2.3	4440	6	2.973530	-0.854327	9.708655	0.004585	*
BQ.1.1.10	705	4	2.831446	2.831446	2.337108	0.182684	*	*
LP.8.1.1	2345	5	2.630623	-0.968622	9.937244	0.004087	*	*
B.1.349	537	3	1.593554	-8.406446	24.812891	0.000002		*
B.1.1.7	477665	3	1.434268	-8.565732	25.131465	0.000002		*
BE.1.1.2	2143	4	1.170904	1.170904	5.658191	0.034735	*	*
BA.5	6418	4	0.522220	0.522220	6.955560	0.018133	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	7	262.228759	NaN	NaN	NaN	*	*	*
LF.7	58	7	258.888377	252.515732	-155.031463	3.579311e-02	*	*
XFG.2	500	7	247.620087	243.532250	-137.064500	4.483978e-06		*
XFG.3.1	87	7	239.640359	233.267714	-116.535427	1.569647e-10		*
XFG.1	14	7	223.714357	217.341712	-84.683424	1.894484e-17		*
LF.7.7.1	188	15	181.719025	156.931077	36.137845	1.100934e-43
LF.7.1	165	15	179.808982	174.816139	0.367721	6.443445e-36
LF.7.1.8	44	15	171.708175	155.753157	38.493687	3.399893e-44
LF.7.6	15	15	168.460035	152.551537	44.896926	1.378959e-45
LF.7.3	54	15	165.118331	149.133983	51.732035	4.533523e-47

Target sequence

, 174_G|T, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10450_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16173_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20235_C|T, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28473_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29137_C|T, 29367_C|T, 29409_C|T, 29510_A|C,
29734_29759

 Case 58 (XFG): USA/CA-LACPHL-AY13111/2025



Target: 530 samples        Number of changes: 157                                                   
BC: KP.3.1 + XFG.2         BC BR: 11-12                    BC BR coord: 4188 - 4189          
Direction L1: <<           Initial region span: 1-11,15-157 Gap history (edge excluded): 11-15
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 2.41e-118 Rec. model vs L2: 4.68e-21                                               
Flags: Model_2BP_Bad_L1_opp

KP.3.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1	1957	11	15.749998	NaN	NaN	NaN	*	*	*
KP.2.2	1334	11	15.576007	15.576007	-7.152014	8.394570e-01	*	*
LF.7.7.1	188	9	15.101403	-2.652858	29.305717	1.015804e-08
LB.1.3.1	292	9	14.642740	5.715886	12.568227	4.383842e-05	*
XEC.2	921	11	14.555106	14.555106	-5.110211	3.027040e-01	*	*
KP.3.1.1	12013	11	14.550812	14.550812	-5.101624	3.011942e-01	*	*
JN.1.11.1	226	9	13.983183	5.059760	13.880480	2.277152e-05	*
XFG.3	480	12	13.775049	5.834013	12.331975	4.942768e-05	*	*
MC.24	831	9	13.219225	4.295802	15.408395	1.059636e-05	*
JN.1	17255	11	13.142408	13.142408	-2.284817	7.353454e-02	*	*

|||||

XFG.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.2	500	15	275.120321	NaN	NaN	NaN	*	*	*
LF.7	58	15	271.173162	257.027123	-180.054246	2.322758e-03	*	*
XFG.3	480	15	270.626033	258.567070	-183.134140	1.083471e-02	*	*
XFG.3.1	87	15	236.922525	224.891019	-115.782037	2.570105e-17		*
XFG.1	14	15	233.734736	221.703229	-109.406459	1.063464e-18		*
LF.7.1	165	23	196.959492	165.285288	3.429425	3.340629e-43
LF.7.7.1	188	15	186.607347	156.607347	20.785305	5.677434e-47		*
LF.7.1.8	44	23	176.438824	144.724215	44.551569	3.933088e-52
LF.7.6	15	15	173.630791	143.630791	46.738419	1.315774e-52		*
LF.7.3	54	15	170.394448	140.394448	53.211105	5.178912e-54		*

Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3717_C|T, 4184_G|A, 4214_T|C, 4222_A|G, 4255_G|A, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T,
8293_C|T, 8326_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 13620_C|A, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 18981_C|T, 19955_C|T, 20055_A|G, 20178_C|T,
21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G,
22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A,
22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A,
23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26196_G|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T,
26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27765_C|T, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C,
28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/CA-LACPHL-AY13137/2025



Target: 530 samples        Number of changes: 158                                                 
BC: LD.1 + XFG.3           BC BR: 4-5                     BC BR coord: 896 - 897           
Direction L1: <<           Initial region span: 1-4,21-158 Gap history (edge excluded): 4-21
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  -                                                                             
Rec. model vs L1: 2.19e-197 Rec. model vs L2: 1.33e-07                                             
Flags: Model_2BP_Bad_L1_opp

LD.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LD.1	70	4	9.085704	NaN	NaN	NaN	*	*	*
KP.2	1589	7	8.894691	6.243829	-4.487657	0.058426	*
XEC.29	135	4	8.457912	8.457912	-8.915824	0.535261	*	*
BA.5.1.17	357	3	8.456578	-1.543422	11.086845	0.000024	*	*
JN.1.29	69	4	7.971640	7.971640	-7.943281	0.327915	*	*
MC.8	93	4	7.731975	7.731975	-7.463950	0.257947	*	*
XEC.39	155	4	7.208205	7.208205	-6.416409	0.153355	*	*
MC.1	932	7	7.060566	6.073660	-4.147321	0.049292	*
KP.3.1.4	511	7	6.889559	5.992689	-3.985378	0.045502	*
MC.9	298	4	6.547233	6.547233	-5.094467	0.078866	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	21	254.192233	NaN	NaN	NaN	*	*	*
LF.7	58	21	252.885348	208.888377	-61.776754	3.543696e-02	*	*
XFG.2	500	21	244.896342	199.918994	-43.837988	4.506454e-06		*
XFG.3.1	87	21	238.660957	189.640359	-23.280718	1.546278e-10		*
XFG.1	14	21	223.954846	173.714357	8.571285	1.875634e-17		*
LF.7.1	165	21	185.740514	131.200980	93.598040	6.443445e-36		*
LF.7.7.1	188	21	181.963602	113.341668	129.316665	1.128804e-43		*
LF.7.1.8	44	21	177.680110	112.172322	131.655356	3.503436e-44		*
LF.7.6	15	21	168.704612	108.924182	138.151636	1.365239e-45		*
LF.7.1.2	26	21	167.580693	102.040983	151.918034	1.396661e-48		*

Target sequence

, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3326_C|A, 3431_G|T, 3565_T|C, 3917_A|G, 3951_3953, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 6268_C|T,
6741_G|A, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T,
12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16173_C|T, 16600_T|C, 17410_C|T, 18048_T|C, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28473_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29137_C|T, 29367_C|T,
29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/CA-LACPHL-AY13158/2025



Target: 530 samples        Number of changes: 154                                           
BC: JN.11 + XFG.2          BC BR: 4-5                    BC BR coord: 2067 - 2068    
Direction L1: <<           Initial region span: 1-4,5-154 Gap history (edge excluded):
Alt. candidates: [], []                                                                            
Model 1BP/2BP comparison:  -                                                                       
Rec. model vs L1: 3.04e-238 Rec. model vs L2: 8.32e-17                                       
Flags: Model_2BP_Bad_L1_opp

JN.11 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.11	67	4	8.712905	NaN	NaN	NaN	*	*	*
KP.2.3.10	10	4	8.417788	8.417788	-2.835576	0.744532	*	*
PL.1.1	12	4	8.235466	8.235466	-2.470933	0.618783	*	*
PD.2	21	4	7.675851	1.065842	11.868317	0.000476	*	*
KP.4.2.4	22	4	7.629331	-0.408730	14.817461	0.000109	*	*
KR.1.4	24	4	7.408788	0.164265	13.671469	0.000194	*	*
KP.3.1.2	28	4	7.277693	7.277693	-0.555386	0.238115	*	*
JN.1.69	32	4	7.254637	7.254637	-0.509274	0.232236	*	*
JN.1.50.2	33	4	7.162322	7.162322	-0.324644	0.211189	*	*
LP.8.1.10	32	4	7.156197	0.546188	12.907624	0.000283	*	*

|||||

XFG.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.2	500	5	294.433454	NaN	NaN	NaN	*	*	*
XFG.3	480	6	287.866398	277.866398	-211.732796	6.364150e-08		*
LF.7	58	6	286.350487	276.350487	-208.700975	1.398892e-08		*
XFG.3.1	87	6	267.087493	257.087493	-170.174985	6.013137e-17		*
XFG.1	14	6	237.190678	227.190678	-110.381355	6.249821e-30		*
LF.7.1	165	12	195.285288	184.660805	-25.321609	2.115063e-48
LF.7.7.1	188	12	186.607347	178.530009	-13.060018	4.603605e-51
LF.7.3	54	12	183.675368	172.993384	-1.986767	1.816679e-53
LF.7.1.8	44	12	174.724215	164.118082	15.763837	2.540473e-57
LF.7.6	15	12	173.630791	163.024657	17.950687	8.498889e-58

Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10570_T|C, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
13378_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 18981_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21127_A|G, 21607_.|GNNNNNNNNNNN,
21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T,
22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28695_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29734_29759

 Case 58 (XFG): USA/CT-DPH-1292714001/2025



Target: 530 samples        Number of changes: 150                                                       
BC: LF.7 + BE.5            BC BR: 147-148                    BC BR coord: 28958 - 28959          
Direction L1: >>           Initial region span: 1-142,148-150 Gap history (edge excluded): 142-148
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 2.88e-07 Rec. model vs L2: 0.00e+00                                                   
Flags: Model_2BP_Bad_L1_opp

LF.7 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	142	309.587062	NaN	NaN	NaN	*	*	*
XFG.3	480	148	308.417909	302.391709	-270.783418	8.543495e-02	*
XFG.2	500	142	300.663746	295.926543	-257.853086	1.330215e-04	*	*
XFG.3.1	87	148	275.208799	269.182598	-204.365197	3.242555e-16
XFG.1	14	148	259.534111	253.507911	-173.015822	5.050348e-23
LF.7.1.8	44	142	224.571938	219.834735	-105.669470	1.197994e-37		*
LF.7.1	165	142	219.939926	215.184485	-96.368970	1.145474e-39		*
LF.7.6	15	142	216.244100	211.506897	-89.013794	2.889226e-41		*
LF.7.7.1	188	142	214.706097	209.968894	-85.937788	6.225003e-42		*
LF.7.3	54	142	206.001218	201.264015	-68.528030	1.031825e-45		*

|||||

BE.5 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
BE.5	231	148	7.835908	NaN	NaN	NaN	*	*	*
JN.1.13.1	751	144	7.032025	1.769229	4.461543	0.002323	*
KP.1.1.3	979	144	6.892653	1.632922	4.734156	0.002029	*
JN.1.2	650	144	6.563489	1.305311	5.389378	0.001459	*
LB.1.3	778	144	6.281969	1.023032	5.953935	0.001103	*
LP.8.1.1	2345	144	4.777156	-0.485641	8.971282	0.000244	*
JN.1	17255	144	4.055319	-1.206550	10.413101	0.000119	*
KP.3.1.1	12013	144	3.973361	-1.289186	10.578372	0.000109	*
JN.1.4	8971	144	3.963317	-1.296691	10.593382	0.000108	*
XFG.3.1	87	144	2.365293	-2.897503	13.795007	0.000022	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12238_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 20270_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T,
25000_C|T, 25207_C|T, 25584_C|T, 25605_A|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28467_A|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29482_C|T, 29510_A|C

 Case 58 (XFG): USA/CT-DPH-1302633001/2025



Target: 530 samples        Number of changes: 154                                                   
BC: KP.3.1.1 + LF.7        BC BR: 12-13                    BC BR coord: 4068 - 4069          
Direction L1: <<           Initial region span: 1-10,13-154 Gap history (edge excluded): 10-13
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 5.39e-135 Rec. model vs L2: 2.90e-27                                               
Flags: Model_2BP_Bad_L1_opp

KP.3.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.1	12013	10	13.891039	NaN	NaN	NaN	*	*	*
KS.1.1.2	252	5	9.308002	-12.386685	54.773370	1.621637e-11
LB.1.3.1	292	5	7.915789	-13.784194	57.568387	3.998907e-12
KP.1.1.1	578	5	7.234155	-14.492697	58.985394	1.966040e-12
BA.2.86.1	1343	5	7.187877	-16.878703	63.757406	1.810506e-13
MC.11.2	146	3	6.967997	-21.114995	72.229989	2.621578e-15
BA.2.47	679	3	6.006357	-58.208586	146.417172	2.034272e-31
BN.1.5	1025	4	5.606905	-63.827622	157.655244	7.373505e-34
MU.2.1.1	10	3	5.379225	-22.676131	75.352263	5.508881e-16
MC.17	46	3	5.239463	-22.815893	75.631787	4.789191e-16

|||||

LF.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	13	308.827859	NaN	NaN	NaN	*	*	*
XFG.2	500	12	306.418196	303.455925	-278.911850	4.630919e-03	*	*
XFG.3	480	13	295.388436	295.388436	-262.776873	1.455734e-06		*
XFG.3.1	87	13	263.410830	263.410830	-198.821659	1.880809e-20		*
XFG.1	14	13	246.254438	246.254438	-164.508877	6.668418e-28		*
LF.7.1.8	44	24	231.469563	210.831531	-93.663062	2.748785e-43
LF.7.1	165	24	224.240243	203.642615	-79.285231	2.083219e-46
LF.7.7.1	188	38	219.628151	200.063133	-72.126265	5.807118e-48
LF.7.6	15	15	204.686595	195.763172	-63.526344	7.879423e-50
LF.7.1.2	26	24	195.403566	174.812055	-21.624110	6.249619e-59

Target sequence

, 186_C|T, 241_C|T, 670_T|G, 813_C|T, 897_C|A, 1177_T|C, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4002_C|T, 4068_C|T, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6543_C|T, 7842_A|G,
7869_C|T, 8152_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10039_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12676_C|T,
12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T,
21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G,
22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A,
22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A,
23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T,
29510_A|C

 Case 58 (XFG): USA/CT-DPH-1304113001/2025



Target: 530 samples        Number of changes: 152                                               
BC: XEC.29 + XFG.3         BC BR: 5-6                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-5,9-152 Gap history (edge excluded): 5-9
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 2.99e-220 Rec. model vs L2: 3.46e-14                                           
Flags: Model_2BP_Bad_L1_opp

XEC.29 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.29	135	5	10.664726	NaN	NaN	NaN	*	*	*
MC.9	298	5	7.269081	7.269081	-4.538162	3.354055e-02	*	*
KP.2	1589	5	7.083669	7.083669	-4.167338	2.787570e-02	*	*
KP.3.1.4	511	5	6.175261	6.175261	-2.350521	1.122064e-02	*	*
MC.1	932	5	5.655268	5.655268	-1.310537	6.670903e-03	*	*
KP.2.2	1334	5	4.924695	4.924695	0.150609	3.214768e-03	*	*
JN.1.39	1007	5	4.819029	4.819029	0.361941	2.894335e-03	*	*
LB.1	1128	5	4.587727	4.587727	0.824545	2.299646e-03	*	*
BF.14	1581	4	4.370988	-5.629012	21.258023	8.378599e-08		*
KP.3.1.1	12013	6	4.091904	3.744455	2.511091	9.878299e-04	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	9	323.955272	NaN	NaN	NaN	*	*	*
LF.7	58	9	309.956453	279.956453	-215.912907	8.315287e-07		*
XFG.2	500	8	298.714244	281.013151	-218.026302	2.400100e-06		*
XFG.3.1	87	9	291.566276	261.566276	-179.132551	8.574360e-15		*
XFG.1	14	9	274.571728	244.571728	-145.143455	3.567525e-22		*
LF.7.7.1	188	17	237.921608	189.544250	-35.088501	4.521819e-46
LF.7.1	165	17	230.871754	202.263752	-60.527503	1.511955e-40
LF.7.1.8	44	17	222.705226	183.169373	-22.338746	7.703460e-49
LF.7.6	15	17	219.416831	179.880978	-15.761956	2.869835e-50
LF.7.3	54	17	215.969767	176.358064	-8.716127	8.494550e-52

Target sequence

, 66_C|T, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1213_C|T, 1288_C|T, 2086_G|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 7842_A|G,
7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25606_G|A, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

 Case 58 (XFG): USA/CT-USAFSAM-S23777/2025



Target: 530 samples        Number of changes: 152                                               
BC: JN.11 + XFG.2          BC BR: 4-5                    BC BR coord: 2067 - 2068        
Direction L1: <<           Initial region span: 1-4,6-152 Gap history (edge excluded): 4-6
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 1.03e-229 Rec. model vs L2: 8.32e-17                                           
Flags: Model_2BP_Bad_L1_opp

JN.11 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.11	67	4	8.712905	NaN	NaN	NaN	*	*	*
KP.2.3.10	10	4	8.417788	8.417788	-2.835576	0.744532	*	*
PL.1.1	12	4	8.235466	8.235466	-2.470933	0.618783	*	*
PD.2	21	4	7.675851	1.065842	11.868317	0.000476	*	*
KP.4.2.4	22	4	7.629331	-0.408730	14.817461	0.000109	*	*
KR.1.4	24	4	7.408788	0.164265	13.671469	0.000194	*	*
KP.3.1.2	28	4	7.277693	7.277693	-0.555386	0.238115	*	*
JN.1.69	32	4	7.254637	7.254637	-0.509274	0.232236	*	*
JN.1.50.2	33	4	7.162322	7.162322	-0.324644	0.211189	*	*
LP.8.1.10	32	4	7.156197	0.546188	12.907624	0.000283	*	*

|||||

XFG.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.2	500	6	309.396975	NaN	NaN	NaN	*	*	*
XFG.3	480	7	303.171216	283.171216	-226.342433	1.828390e-11		*
LF.7	58	7	302.503793	282.503793	-225.007587	9.402928e-12		*
XFG.3.1	87	7	269.640359	249.640359	-159.280718	5.013892e-26		*
XFG.1	14	7	253.714357	233.714357	-127.428715	6.081845e-33		*
LF.7.7.1	188	13	213.692328	205.090802	-70.181604	2.250898e-45
LF.7.1	165	13	211.503267	190.878784	-41.757568	1.517159e-51
LF.7.1.8	44	13	204.724215	184.118082	-28.236163	1.758735e-54
LF.7.1.2	26	13	195.612259	174.927683	-9.855367	1.794875e-58
LF.7.6	15	13	189.530316	168.924182	2.151636	4.426861e-61

Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2334_C|T, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21846_C|A, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G,
22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23592_A|C, 23599_T|G, 23604_C|G, 23635_C|T, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/MA-MASPHL-14177/2025



Target: 530 samples         Number of changes: 156                                                            
BC: XFG.3 + KP.3.1.5 + XFG.3 BC BR: 5-6, 9-10                   BC BR coord: 896 - 897, 3430 - 3431     
Direction L1: <<            Initial region span: 1-5,7-9,10-156 Gap history (edge excluded): 5-10 -> 5-7
Alt. candidates: [], []                                                                                              
Model 1BP/2BP comparison:   2BP vs 1BP: 2.86e-02                                                                     
Rec. model vs L1: 5.55e-09  Rec. model vs L2: 1.44e-217                                                       
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	5	9.640979	None	None	None	*	*	*

|||||

KP.3.1.5 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.5	45	7	7.613984	NaN	NaN	NaN	*	*	*
XBB.2.3.14	18	7	7.613984	-2.386016	22.772033	1.000000e+00	*	*
NL.11	57	7	7.208518	-2.791482	23.582963	6.669768e-01	*	*
XBB.4	49	6	6.609415	6.609415	4.781171	8.062670e+03	*	*
B.1.1.304	143	8	6.536776	-19.539319	57.078638	3.545505e-08		*
AZ.5	21	8	6.536776	-23.368480	64.736960	7.697156e-10		*
B.1.1.434	1274	8	6.534418	-27.588067	73.176135	1.131378e-11		*
XBB.1.5.92	41	6	6.272764	6.272764	5.454472	5.767535e+03	*	*
JE.1.1.1	46	7	5.577102	-11.675249	41.350497	9.234306e-05	*	*
LE.1.2	19	7	5.362692	-12.680191	43.360383	3.380168e-05	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	10	279.842351	NaN	NaN	NaN	*	*	*
LF.7	58	10	269.362742	279.250049	-204.500098	3.589186e-05	*	*
XFG.2	500	10	251.669760	259.218842	-164.437684	7.179224e-14		*
XFG.3.1	87	10	239.813677	248.482412	-142.964825	1.555087e-18		*
XFG.1	14	10	218.661809	226.646956	-99.293912	5.116050e-28		*
LF.7.1	165	18	186.187225	188.465008	-22.930015	1.341441e-44
LF.7.1.2	26	18	181.834837	183.570539	-13.141078	1.003922e-46
LF.7.7.1	188	14	180.598486	177.956410	-1.912821	3.657097e-49
LF.7.1.8	44	18	177.515938	178.161865	-2.323731	4.489178e-49
LF.7.1.5	40	18	156.918808	157.072878	39.854244	3.126566e-58

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2485_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17007_T|C, 17410_C|T, 18129_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19593_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN,
21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T,
22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23373_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27754_G|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A,
29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/MD-MDH-11764/2025



Target: 530 samples        Number of changes: 146                                               
BC: LF.1 + LF.7            BC BR: 5-6                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-5,9-146 Gap history (edge excluded): 5-9
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 2.10e-138 Rec. model vs L2: 1.23e-07                                           
Flags: Model_2BP_Bad_L1_opp

LF.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.1	141	5	12.979047	NaN	NaN	NaN	*	*	*
MC.6	366	5	11.261938	11.261938	-8.523876	1.790661e-01	*	*
MC.10.1	650	5	9.038076	9.038076	-4.076152	1.944821e-02	*	*
JN.1.4.4	32	4	8.345935	6.143533	1.712934	1.075467e-03	*	*
BF.40	56	4	8.145755	-1.854245	17.708490	3.607791e-07		*
FL.5.1	10	4	6.948982	-3.051018	20.102037	1.092093e-07		*
BQ.1.1.41	818	4	6.470822	-3.529178	21.058357	6.757687e-08		*
GS.1	109	4	5.997751	-4.002249	22.004497	4.223570e-08		*
BE.1.2	467	4	5.878484	-4.121516	22.243032	3.745971e-08		*
BQ.1.1.4	2753	4	5.833933	-4.166067	22.332134	3.581138e-08		*

|||||

LF.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	9	252.204253	NaN	NaN	NaN	*	*	*
XFG.3	480	9	242.615949	221.553098	-93.106196	6.806823e-05	*	*
XFG.2	500	9	225.532594	196.930693	-43.861386	1.375444e-15		*
XFG.1	14	9	216.855594	195.782273	-41.564545	4.355161e-16		*
XFG.3.1	87	9	209.047999	187.974677	-25.949355	1.775562e-19		*
LF.7.1.8	44	17	188.979180	161.316976	27.366048	4.688618e-31
LF.7.7.1	188	13	166.904493	135.307771	79.384457	2.383509e-42
LF.7.1.2	26	17	165.871947	138.256263	73.487475	4.531209e-41
LF.7.1.5	40	17	160.276110	132.660426	84.679149	1.683978e-43
LF.7.1	165	17	158.101789	130.461639	89.076722	1.865901e-44

Target sequence

, 44_C|T, 241_C|T, 481_A|G, 670_T|G, 897_C|A, 2485_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19593_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22910_A|G,
22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23148_A|C, 23222_G|A, 23271_C|T,
23277_C|T, 23373_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27754_G|C, 27807_C|T, 27810_T|C, 28271_A|T,
28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/MI-UM-10064755202/2025



Target: 530 samples       Number of changes: 153                                                                          
BC: XFG.3 + NY.15 + XFG.3 BC BR: 134-135, 146-147                   BC BR coord: 26872 - 26873, 28880 - 28881      
Direction L1: >>          Initial region span: 1-134,136-146,147-153 Gap history (edge excluded): 134-147 -> 134-136
Alt. candidates: [], []                                                                                                          
Model 1BP/2BP comparison: 2BP vs 1BP: 1.26e-01                                                                                   
Rec. model vs L1: 3.43e-22 Rec. model vs L2: 1.17e-180                                                                     
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	134	287.998031	NaN	NaN	NaN	*	*	*
LF.7	58	139	281.013438	284.704425	-247.408850	4.882614e-08
XFG.2	500	134	264.611688	278.175804	-234.351608	7.123762e-11		*
XFG.3.1	87	134	238.035180	250.992096	-179.984191	1.112792e-22		*
XFG.1	14	134	222.185044	235.870198	-149.740397	3.019127e-29		*
LF.7.1.8	44	134	213.864314	211.349996	-100.699992	6.776114e-40		*
LF.7.7.1	188	134	188.199426	192.510309	-63.020618	4.455256e-48		*
LF.7.1	165	134	183.904396	193.083008	-64.166015	7.917571e-48		*
LF.7.6	15	134	180.184030	177.699883	-33.399766	1.648054e-54		*
LF.7.3	54	134	170.077623	167.698837	-13.397673	7.482152e-59		*

|||||

NY.15 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
NY.15	216	136	15.911165	NaN	NaN	NaN	*	*	*
KP.3.1.11	31	141	12.700518	-1.884552	27.769104	4.117888e-04	*
MD.1.1	24	141	12.312095	-2.272976	28.545951	2.788044e-04	*
LF.9	48	141	10.653867	-3.931204	31.862407	5.327731e-05	*
JN.1.16.3	52	141	10.573824	-4.030664	32.061329	4.820730e-05	*
JN.1.4	8971	136	10.231699	9.001183	5.997634	2.197708e+01	*	*
CM.8.1	200	135	10.147548	10.147548	3.704904	6.940785e+01	*	*
CM.4	76	143	10.147058	-13.794824	51.589649	2.768390e-09
CM.8.1.4	19	143	10.147058	-13.954338	51.908676	2.359066e-09
CM.6.1	14	143	10.147058	-13.674353	51.348706	3.121351e-09

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	147	13.542054	None	None	None	*	*	*

Target sequence

, 241_C|T, 509_523, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7113_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9079_A|G, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10039_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21483_T|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27059_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27577_C|T, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28550_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/MI-UM-10064755202/2025



Target: 530 samples       Number of changes: 153                                                                          
BC: XFG.3 + NY.15 + XFG.3 BC BR: 134-135, 146-147                   BC BR coord: 26872 - 26873, 28880 - 28881      
Direction L1: >>          Initial region span: 1-134,136-146,147-153 Gap history (edge excluded): 134-147 -> 134-136
Alt. candidates: [], []                                                                                                          
Model 1BP/2BP comparison: 2BP vs 1BP: 1.26e-01                                                                                   
Rec. model vs L1: 3.43e-22 Rec. model vs L2: 1.17e-180                                                                     
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	134	287.998031	NaN	NaN	NaN	*	*	*
LF.7	58	139	281.013438	284.704425	-247.408850	4.882614e-08
XFG.2	500	134	264.611688	278.175804	-234.351608	7.123762e-11		*
XFG.3.1	87	134	238.035180	250.992096	-179.984191	1.112792e-22		*
XFG.1	14	134	222.185044	235.870198	-149.740397	3.019127e-29		*
LF.7.1.8	44	134	213.864314	211.349996	-100.699992	6.776114e-40		*
LF.7.7.1	188	134	188.199426	192.510309	-63.020618	4.455256e-48		*
LF.7.1	165	134	183.904396	193.083008	-64.166015	7.917571e-48		*
LF.7.6	15	134	180.184030	177.699883	-33.399766	1.648054e-54		*
LF.7.3	54	134	170.077623	167.698837	-13.397673	7.482152e-59		*

|||||

NY.15 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
NY.15	216	136	15.911165	NaN	NaN	NaN	*	*	*
KP.3.1.11	31	141	12.700518	-1.884552	27.769104	4.117888e-04	*
MD.1.1	24	141	12.312095	-2.272976	28.545951	2.788044e-04	*
LF.9	48	141	10.653867	-3.931204	31.862407	5.327731e-05	*
JN.1.16.3	52	141	10.573824	-4.030664	32.061329	4.820730e-05	*
JN.1.4	8971	136	10.231699	9.001183	5.997634	2.197708e+01	*	*
CM.8.1	200	135	10.147548	10.147548	3.704904	6.940785e+01	*	*
CM.4	76	143	10.147058	-13.794824	51.589649	2.768390e-09
CM.8.1.4	19	143	10.147058	-13.954338	51.908676	2.359066e-09
CM.6.1	14	143	10.147058	-13.674353	51.348706	3.121351e-09

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	147	13.542054	None	None	None	*	*	*

Target sequence

 Case 58 (XFG): USA/MN-MDH-47445/2025



Target: 530 samples        Number of changes: 153                                           
BC: MC.33 + XFG.3          BC BR: 5-6                    BC BR coord: 1426 - 1427    
Direction L1: <<           Initial region span: 1-5,6-153 Gap history (edge excluded):
Alt. candidates: [], []                                                                            
Model 1BP/2BP comparison:  1BP vs 2BP: 3.62e-01                                                    
Rec. model vs L1: 2.16e-233 Rec. model vs L2: 1.37e-15                                       
Flags: Model_1BP_Best

MC.33 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.33	31	5	12.303173	NaN	NaN	NaN	*	*	*
KP.4.1.1	12	4	9.895496	-0.104504	10.209008	4.077608e-06		*
NY.12	62	4	9.335620	-0.664380	11.328760	2.329167e-06		*
JN.13	15	4	9.161527	-0.838473	11.676947	1.955235e-06		*
LF.7.1	165	5	7.947883	7.947883	-5.895765	1.284244e-02	*	*
MD.1	19	4	7.826526	-2.173474	14.346949	5.145362e-07		*
KP.2.3.13	25	4	7.552089	-2.447911	14.895822	3.908273e-07		*
MC.29	54	4	7.475128	-2.524872	15.049744	3.625875e-07		*
XFJ.1	59	4	7.334994	-2.665006	15.330012	3.152184e-07		*
KP.3.2	737	5	7.309689	7.309689	-4.619377	6.771721e-03	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	6	320.978235	NaN	NaN	NaN	*	*	*
XFG.2	500	6	312.095267	304.556637	-269.113274	7.357210e-08		*
LF.7	58	6	295.993193	295.993193	-251.986386	1.409783e-11		*
XFG.3.1	87	6	262.157898	262.157898	-184.315796	2.849696e-26		*
XFG.1	14	6	247.211449	247.211449	-154.422899	9.164232e-33		*
LF.7.1	165	1	212.378145	204.430262	-68.860524	2.415339e-51
LF.7.1.8	44	16	202.916100	197.408311	-54.816622	2.158892e-54
LF.7.7.1	188	12	196.168587	186.726282	-33.452563	4.940767e-59
LF.7.6	15	12	182.840632	182.234498	-24.468997	5.543858e-61
LF.7.1.2	26	16	181.151893	175.612183	-11.224366	7.355482e-64

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1288_C|T, 1426_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6541_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 17825_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19217_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28281_A|G, 28297_T|C, 28311_C|T, 28362_28370, 28528_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/MN-MDH-47488/2025



Target: 530 samples        Number of changes: 153                                               
BC: KP.4.1.1 + XFG.2       BC BR: 6-7                    BC BR coord: 3037 - 3038        
Direction L1: <<           Initial region span: 1-6,8-153 Gap history (edge excluded): 6-8
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  1BP vs 2BP: 1.16e-01                                                        
Rec. model vs L1: 1.54e-218 Rec. model vs L2: 2.58e-11                                           
Flags: Model_1BP_Best

KP.4.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.4.1.1	12	6	10.976590	NaN	NaN	NaN	*	*	*
JN.13	15	6	10.242621	10.242621	-6.485242	0.481909	*	*
JN.1.46	308	7	9.884875	7.197732	-0.395465	0.022937	*	*
MC.33	31	6	9.804366	9.804366	-5.608732	0.310367	*	*
NY.12	62	4	9.335620	4.042019	5.915962	0.000973	*
MD.1	19	6	8.907620	8.907620	-3.815240	0.126818	*	*
JN.18	316	7	8.745078	6.083578	1.832845	0.007521	*	*
KP.2.3.13	25	6	8.633183	8.633183	-3.266366	0.096328	*	*
MC.24	831	7	8.586741	6.892128	0.215744	0.016823	*	*
XFJ.1	59	6	8.416088	8.416088	-2.832176	0.077305	*	*

|||||

XFG.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.2	500	8	311.024223	NaN	NaN	NaN	*	*	*
XFG.3	480	8	306.810313	296.810313	-257.620627	1.477232e-02	*	*
LF.7	58	8	294.929491	284.929491	-233.858981	1.023364e-07		*
XFG.3.1	87	17	261.178496	251.076804	-166.153608	2.027639e-22
XFG.1	14	17	247.451939	236.130355	-136.260711	6.553293e-29
LF.7.1	165	17	219.915996	193.349168	-50.698336	1.727196e-47
LF.7.1.8	44	17	212.916100	186.327217	-36.654434	1.536112e-50
LF.7.7.1	188	17	205.348216	175.645188	-15.290375	3.533116e-55
LF.7.6	15	17	192.014928	171.153404	-6.306808	3.964383e-57
LF.7.1.2	26	17	191.151893	164.570310	6.859381	5.474525e-60

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3092_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5037_G|A, 5239_C|T, 6183_A|G, 6541_C|T, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 17825_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24902_A|G, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28281_A|G, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/MN-MDH-47506/2025



Target: 530 samples        Number of changes: 150                                               
BC: JN.11 + LF.7           BC BR: 4-5                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-4,6-150 Gap history (edge excluded): 4-6
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 1.94e-228 Rec. model vs L2: 4.16e-08                                           
Flags: Model_2BP_Bad_L1_opp

JN.11 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.11	67	4	8.712905	NaN	NaN	NaN	*	*	*
KP.2.3.10	10	4	8.417788	8.417788	-8.835576	0.744532	*	*
PL.1.1	12	4	8.235466	8.235466	-8.470933	0.618783	*	*
PD.2	21	4	7.675851	7.675851	-7.351701	0.353455	*	*
KP.4.2.4	22	4	7.629331	7.629331	-7.258661	0.337902	*	*
KR.1.4	24	4	7.408788	7.408788	-6.817576	0.271173	*	*
KP.3.1.2	28	4	7.277693	7.277693	-6.555386	0.238115	*	*
JN.1.69	32	4	7.254637	7.254637	-6.509274	0.232236	*	*
JN.1.50.2	33	4	7.162322	7.162322	-6.324644	0.211189	*	*
LP.8.1.10	32	4	7.156197	7.156197	-6.312394	0.210136	*	*

|||||

LF.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	6	325.993193	NaN	NaN	NaN	*	*	*
XFG.3	480	6	325.966793	315.966793	-293.933586	9.704455e-01	*	*
XFG.2	500	5	321.585552	314.046922	-290.093844	1.422741e-01	*	*
XFG.3.1	87	6	292.157898	282.157898	-226.315796	2.021372e-15		*
XFG.1	14	6	277.211449	267.211449	-196.422899	6.500454e-22		*
LF.7.1	165	12	235.054745	224.430262	-110.860524	1.713270e-40
LF.7.1.8	44	12	228.014445	217.408311	-96.816622	1.531364e-43
LF.7.7.1	188	12	226.168587	218.091249	-98.182497	3.022726e-43
LF.7.6	15	12	212.840632	202.234498	-66.468997	3.932419e-50
LF.7.3	54	12	209.604289	198.922305	-59.844610	1.428807e-51

Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18636_G|A, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/MN-MDH-47532/2025



Target: 530 samples        Number of changes: 154                                                   
BC: LF.7.7.1 + XFG.2       BC BR: 10-11                    BC BR coord: 3566 - 3567          
Direction L1: <<           Initial region span: 1-10,12-154 Gap history (edge excluded): 10-12
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 4.77e-63 Rec. model vs L2: 3.13e-16                                               
Flags: Model_2BP_Bad_L1_opp

LF.7.7.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7.7.1	188	10	14.577215	NaN	NaN	NaN	*	*	*
LB.1.3.1	292	10	14.371388	14.371388	-8.742775	0.814647	*	*
LB.1.3	778	10	12.936862	12.936862	-5.873723	0.193980	*	*
KP.3.1.1	12013	10	12.053449	12.053449	-4.106898	0.080460	*	*
KP.2.2	1334	10	11.322836	11.322836	-2.645672	0.038774	*	*
KP.1.1.1	578	10	11.188305	11.188305	-2.376610	0.033878	*	*
XEC.2	921	10	10.708486	10.708486	-1.416972	0.020963	*	*
LB.1.7	1971	10	10.525027	10.525027	-1.050055	0.017422	*	*
KP.1.1.3	979	10	10.313570	10.313570	-0.627140	0.014122	*	*
JN.1	17255	10	10.293289	10.293289	-0.586578	0.013843	*	*

|||||

XFG.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.2	500	12	306.368618	NaN	NaN	NaN	*	*	*
LF.7	58	12	297.746406	287.746406	-243.492811	1.795602e-04	*	*
XFG.3	480	12	297.741957	287.741957	-243.483913	1.786646e-04	*	*
XFG.3.1	87	12	264.002452	254.002452	-176.004904	3.971392e-19		*
XFG.1	14	12	248.894160	238.894160	-145.788321	1.093767e-25		*
LF.7.1	165	14	215.054745	196.131322	-60.262644	2.926315e-44
LF.7.1.8	44	14	208.014445	189.091022	-46.182044	2.563823e-47
LF.7.7.1	188	14	206.168587	178.414326	-24.828652	5.926447e-52
LF.7.6	15	14	192.840632	173.917209	-15.834418	6.583688e-54
LF.7.3	54	14	189.604289	170.662174	-9.324348	2.540041e-55

Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2334_C|T, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3931_T|A, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11541_T|G, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16323_C|T, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT,
21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T,
22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25520_T|C, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T,
26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29734_29759

 Case 58 (XFG): USA/MN-MDH-47545/2025



Target: 530 samples        Number of changes: 152                                               
BC: XFG.3 + PQ.5           BC BR: 145-146                    BC BR coord: 28361 - 28362  
Direction L1: >>           Initial region span: 1-145,146-152 Gap history (edge excluded):
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 4.24e-35 Rec. model vs L2: 0.00e+00                                           
Flags: Model_2BP_Bad_L1_opp

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	145	287.019003	NaN	NaN	NaN	*	*	*
XFG.2	500	145	283.539487	283.539487	-237.078974	3.080741e-02	*	*
LF.7	58	145	279.587062	279.587062	-229.174125	5.902290e-04	*	*
XFG.3.1	87	145	243.919801	243.919801	-157.839603	1.913850e-19		*
XFG.1	14	145	228.245114	228.245114	-126.490229	2.980862e-26		*
LF.7.1.8	44	145	208.605626	208.605626	-87.211252	8.806396e-35		*
LF.7.6	15	145	200.443583	200.443583	-70.887166	2.517417e-38		*
LF.7.1	165	145	189.939926	189.939926	-49.879851	6.897500e-43		*
LF.7.7.1	188	145	184.706097	184.706097	-39.412194	3.674177e-45		*
LF.7.3	54	145	176.001218	176.001218	-22.002436	6.090131e-49		*

|||||

PQ.5 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
PQ.5	11	146	16.976002	NaN	NaN	NaN	*	*	*
PQ.14	26	146	16.936781	16.936781	-19.873562	9.607894e-01	*	*
PQ.12	17	146	16.915377	16.915377	-19.830754	9.417645e-01	*	*
PQ.10	24	146	16.888990	16.888990	-19.777980	9.185123e-01	*	*
PQ.1	52	146	16.773809	16.773809	-19.547619	8.187308e-01	*	*
NB.1.8.1	357	146	16.760158	16.760158	-19.520315	8.065414e-01	*	*
PQ.2	91	146	16.746984	16.746984	-19.493968	7.945336e-01	*	*
PQ.8	13	146	16.728905	16.728905	-19.457810	7.827045e-01	*	*
PQ.4	29	146	16.635001	16.635001	-19.270001	7.117703e-01	*	*
DV.7.1.1	23	147	8.685330	-1.314670	16.629341	1.139604e-08		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4714_T|C, 5239_C|T, 6183_A|G, 6543_C|T, 7842_A|G, 7869_C|T, 8152_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10039_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 14781_T|C, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23593_G|C, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28432_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 29164_T|C, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/NJ-GBW-GKISBBBH44036/2025



Target: 530 samples        Number of changes: 151                                                      
BC: XFG.3 + HV.1.11 + XFG.3 BC BR: 6-7, 8-9                   BC BR coord: 896 - 897, 2789 - 2790
Direction L1: <<           Initial region span: 1-6,7-8,9-151 Gap history (edge excluded): 6-9 ->
Alt. candidates: [], []                                                                                       
Model 1BP/2BP comparison:  2BP vs 1BP: 1.47e-10                                                               
Rec. model vs L1: 1.39e-16 Rec. model vs L2: 0.00e+00                                                  
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	6	9.468747	None	None	None	*	*	*

|||||

HV.1.11 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
HV.1.11	24	7	8.135609	NaN	NaN	NaN	*	*	*
HK.1	30	7	7.219319	7.219319	-6.438637	4.005166e-01	*	*
HV.1.1	536	7	6.732410	6.732410	-5.464820	2.453671e-01	*	*
EG.5.1.16	519	7	5.976122	5.976122	-3.952243	1.153251e-01	*	*
B.1.1.428	42	8	5.908262	-10.951078	29.902156	5.146237e-09		*
A.27	515	8	5.908262	-12.451723	32.903445	1.148281e-09		*
AY.71	260	8	5.908262	-4.091738	16.183477	4.906253e-06		*
AY.72	300	8	5.908262	-4.091738	16.183477	4.906253e-06		*
AY.73	462	8	5.908262	-4.091738	16.183477	4.906253e-06		*
B.1.1.181	17	8	5.908262	-4.091738	16.183477	4.906253e-06		*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	9	315.994603	NaN	NaN	NaN	*	*	*
LF.7	58	9	315.327180	315.214487	-286.428974	3.535750e-05	*	*
XFG.2	500	8	312.290173	309.452453	-274.904907	1.108597e-07		*
XFG.3.1	87	9	282.463746	281.132481	-218.264963	5.566140e-20		*
XFG.1	14	9	266.537744	264.522890	-185.045781	3.420537e-27		*
LF.7.1	165	15	224.326654	234.135537	-124.271074	2.167130e-40
LF.7.1.8	44	15	217.547602	214.176278	-84.352557	4.649081e-49
LF.7.7.1	188	1	215.652269	214.811489	-85.622979	8.772919e-49
LF.7.6	15	15	202.353703	200.916485	-57.832971	8.102560e-55
LF.7.3	54	15	199.011999	196.199305	-48.398611	7.259786e-57

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2334_C|T, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|A, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/NJ-GBW-GKPLAAAA70247/2025



Target: 530 samples        Number of changes: 152                                                      
BC: XFG.3 + HV.1.11 + XFG.3 BC BR: 6-7, 8-9                   BC BR coord: 896 - 897, 2789 - 2790
Direction L1: <<           Initial region span: 1-6,7-8,9-152 Gap history (edge excluded): 6-9 ->
Alt. candidates: [], []                                                                                       
Model 1BP/2BP comparison:  2BP vs 1BP: 1.47e-10                                                               
Rec. model vs L1: 1.39e-16 Rec. model vs L2: 0.00e+00                                                  
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	6	9.468747	None	None	None	*	*	*

|||||

HV.1.11 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
HV.1.11	24	7	8.135609	NaN	NaN	NaN	*	*	*
HK.1	30	7	7.219319	7.219319	-6.438637	4.005166e-01	*	*
HV.1.1	536	7	6.732410	6.732410	-5.464820	2.453671e-01	*	*
EG.5.1.16	519	7	5.976122	5.976122	-3.952243	1.153251e-01	*	*
B.1.1.428	42	8	5.908262	-10.951078	29.902156	5.146237e-09		*
A.27	515	8	5.908262	-12.451723	32.903445	1.148281e-09		*
AY.71	260	8	5.908262	-4.091738	16.183477	4.906253e-06		*
AY.72	300	8	5.908262	-4.091738	16.183477	4.906253e-06		*
AY.73	462	8	5.908262	-4.091738	16.183477	4.906253e-06		*
B.1.1.181	17	8	5.908262	-4.091738	16.183477	4.906253e-06		*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	9	320.273315	NaN	NaN	NaN	*	*	*
LF.7	58	9	320.178790	320.066097	-294.132194	6.283489e-05	*	*
XFG.2	500	8	314.987618	312.149898	-278.299797	2.294880e-08		*
XFG.3.1	87	9	285.811278	284.480014	-222.960028	2.207149e-20		*
XFG.1	14	9	256.537744	254.522890	-163.045781	2.160432e-33		*
LF.7.1	165	15	228.643587	238.452470	-130.904940	2.255572e-40
LF.7.7.1	188	1	220.021027	219.180248	-92.360495	9.647218e-49
LF.7.1.8	44	15	207.547602	204.176278	-62.352557	2.936388e-55
LF.7.1.2	26	15	201.202901	198.835611	-51.671222	1.408254e-57
PC.3	42	15	199.379236	196.551829	-47.103658	1.433237e-58

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2334_C|T, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|A, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 13427_G|A, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/NJ-PHEL-V25011860/2025



Target: 530 samples        Number of changes: 150                                               
BC: JN.1.53.1 + LF.7       BC BR: 4-5                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-4,6-150 Gap history (edge excluded): 4-6
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 9.44e-201 Rec. model vs L2: 6.10e-09                                           
Flags: Model_2BP_Bad_L1_opp

JN.1.53.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.53.1	12	4	10.761787	NaN	NaN	NaN	*	*	*
JN.4	91	4	9.333671	9.333671	-10.667342	0.240508	*	*
NL.18	10	4	8.546213	8.546213	-9.092426	0.109154	*	*
XEC.17	13	4	8.283849	8.283849	-8.567698	0.084163	*	*
LD.2	13	4	8.283849	8.283849	-8.567698	0.084163	*	*
JN.1.1.10	17	4	8.015585	8.015585	-8.031170	0.064248	*	*
JN.1.64.1	14	4	7.901440	7.901440	-7.802879	0.057269	*	*
MC.10.1.5	19	4	7.850292	7.850292	-7.700584	0.054476	*	*
JN.1.7.2	180	5	7.462227	5.610990	-3.221981	0.005799	*	*
XEC.2	921	5	7.340305	3.986077	0.027846	0.001142	*	*

|||||

LF.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	6	346.907477	NaN	NaN	NaN	*	*	*
XFG.3	480	1	320.935805	315.176827	-290.353655	3.654104e-10
XFG.2	500	6	308.801106	291.262476	-242.524952	1.501856e-20		*
XFG.3.1	87	3	288.165668	283.451414	-226.902828	6.092401e-24
XFG.1	14	6	264.571728	254.571728	-169.143455	1.747285e-36		*
LF.7.1	165	16	227.427289	211.941555	-83.883111	5.350447e-55
LF.7.1.8	44	16	220.622921	205.115133	-70.230265	5.812062e-58
LF.7.7.1	188	12	218.986556	199.544250	-59.088501	2.214675e-60
LF.7.1.2	26	16	213.318683	197.778973	-55.557947	3.791231e-61
LF.7.6	15	12	200.487112	189.880978	-39.761956	1.405574e-64

Target sequence

, 241_C|T, 583_C|T, 670_T|G, 897_C|A, 2445_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6673_T|C, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22883_C|A,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24034_C|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

 Case 58 (XFG): USA/NJ-PHEL-V25012011/2025



Target: 530 samples        Number of changes: 150                                           
BC: JN.1.7.8 + XFG.3       BC BR: 4-5                    BC BR coord: 896 - 897      
Direction L1: <<           Initial region span: 1-4,5-150 Gap history (edge excluded):
Alt. candidates: [], []                                                                            
Model 1BP/2BP comparison:  -                                                                       
Rec. model vs L1: 9.80e-210 Rec. model vs L2: 1.27e-14                                       
Flags: Model_2BP_Bad_L1_opp

JN.1.7.8 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.7.8	34	4	10.445059	NaN	NaN	NaN	*	*	*
JN.1.11	43	4	9.890658	9.890658	-9.781316	5.740723e-01	*	*
MC.37	21	3	8.888229	-4.739126	19.478252	2.542367e-07		*
KP.2.3.3	149	4	7.472009	7.472009	-4.944018	5.104743e-02	*	*
LA.1	149	4	7.449603	7.449603	-4.899205	5.003663e-02	*	*
JN.1.16.1	466	4	5.159737	5.159737	-0.319475	5.067032e-03	*	*
KP.3.2	737	4	4.943160	4.943160	0.113679	4.086771e-03	*	*
MC.10.1	650	4	4.484871	4.484871	1.030257	2.579912e-03	*	*
BA.5.2.23	644	3	4.295678	-5.704322	21.408643	9.685992e-08		*
LB.1.3	778	4	4.119803	4.119803	1.760394	1.790966e-03	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	5	303.613273	NaN	NaN	NaN	*	*	*
LF.7	58	5	303.571870	303.571870	-267.143740	9.559975e-01	*	*
XFG.2	500	5	298.801106	291.262476	-242.524952	4.308159e-06		*
XFG.3.1	87	5	282.540815	282.540815	-225.081629	7.034671e-10		*
XFG.1	14	5	254.571728	254.571728	-169.143455	5.012185e-22		*
LF.7.1.8	44	11	219.754954	219.148820	-98.297641	2.076427e-37
LF.7.1	165	11	212.566038	211.941555	-83.883111	1.534806e-40
LF.7.7.1	188	11	208.986556	199.544250	-59.088501	6.352918e-46
LF.7.6	15	11	190.487112	189.880978	-39.761956	4.031968e-50
LF.7.3	54	11	187.040048	186.358064	-32.716127	1.193440e-51

Target sequence

, 241_C|T, 670_T|G, 896_G|A, 897_C|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10039_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 17550_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19648_G|T, 19955_C|T, 20055_A|G, 20178_C|T, 20670_G|A, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

 Case 58 (XFG): USA/NJ-PHEL-V25012357/2025



Target: 530 samples        Number of changes: 151                                               
BC: JN.4 + LF.7            BC BR: 5-6                    BC BR coord: 1514 - 1515        
Direction L1: <<           Initial region span: 1-5,7-151 Gap history (edge excluded): 5-7
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 6.49e-238 Rec. model vs L2: 2.40e-15                                           
Flags: Model_2BP_Bad_L1_opp

JN.4 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.4	91	5	11.875704	NaN	NaN	NaN	*	*	*
JN.1.53.1	12	4	10.761787	0.761787	10.476426	1.488733e-05	*	*
NL.18	10	4	8.546213	-1.453787	14.907574	1.625004e-06		*
LD.2	13	4	8.283849	-8.043214	28.086428	2.232821e-09		*
XEC.17	13	4	8.283849	-1.716151	15.432302	1.252962e-06		*
JN.1.1.10	17	4	8.015585	-1.984415	15.968830	9.564857e-07		*
JN.1.64.1	14	4	7.901440	-2.098560	16.197121	8.525790e-07		*
MC.10.1.5	19	4	7.850292	-2.149708	16.299416	8.109982e-07		*
KP.4.1.2	32	4	7.286775	-2.713225	17.426450	4.609391e-07		*
JN.1.18.5	37	4	7.237880	-2.762120	17.524239	4.406566e-07		*

|||||

LF.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	7	346.907477	NaN	NaN	NaN	*	*	*
XFG.3	480	6	315.176827	315.176827	-290.353655	3.654104e-10		*
XFG.2	500	7	308.801106	291.262476	-242.524952	1.501856e-20		*
XFG.3.1	87	6	283.451414	283.451414	-226.902828	6.092401e-24		*
XFG.1	14	7	264.571728	254.571728	-169.143455	1.747285e-36		*
LF.7.1	165	17	227.427289	211.941555	-83.883111	5.350447e-55
LF.7.1.8	44	17	220.622921	205.115133	-70.230265	5.812062e-58
LF.7.7.1	188	13	218.986556	199.544250	-59.088501	2.214675e-60
LF.7.1.2	26	17	213.318683	197.778973	-55.557947	3.791231e-61
LF.7.6	15	13	200.487112	189.880978	-39.761956	1.405574e-64

Target sequence

, 241_C|T, 583_C|T, 670_T|G, 897_C|A, 1514_C|T, 2445_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6673_T|C, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22883_C|A, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24034_C|T,
24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

 Case 58 (XFG): USA/NY-PRL-250520_81F07/2025



Target: 530 samples        Number of changes: 155                                               
BC: KS.1.3 + XFG.3         BC BR: 4-5                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-4,9-155 Gap history (edge excluded): 4-9
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 2.00e-214 Rec. model vs L2: 1.13e-08                                           
Flags: Model_2BP_Bad_L1_opp

KS.1.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KS.1.3	45	4	10.286720	NaN	NaN	NaN	*	*	*
KP.3.1	1957	8	8.879327	4.771811	-1.543623	0.004026	*
KP.3.2.9	28	4	8.768748	8.768748	-9.537496	0.219808	*	*
LK.2.1	10	4	8.699755	8.699755	-9.399510	0.204948	*	*
PR.2	20	4	8.648462	8.648462	-9.296923	0.194952	*	*
KR.1.1	33	4	8.541924	8.541924	-9.083849	0.174645	*	*
JN.2.5	25	4	8.435789	8.435789	-8.871579	0.157237	*	*
KP.2.15	253	4	8.319432	8.319432	-8.638864	0.140156	*	*
JN.1.16.5	24	4	7.781727	7.781727	-7.563453	0.081676	*	*
LF.7.3.1	26	4	7.705023	7.705023	-7.410046	0.075774	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	9	285.079706	NaN	NaN	NaN	*	*	*
LF.7	58	9	257.824674	238.888377	-127.776754	5.634715e-17		*
XFG.2	500	9	255.322126	238.966995	-127.933989	6.073570e-17		*
XFG.3.1	87	18	238.660957	219.640359	-89.280718	2.458687e-25
XFG.1	14	18	223.954846	203.714357	-57.428715	2.982384e-32
LF.7.1.8	44	18	204.917733	169.409944	11.180111	3.767830e-47
LF.7.7.1	188	18	203.503019	164.881084	20.237832	4.061976e-49
LF.7.1	165	18	185.740514	150.254780	49.490440	1.807926e-55
LF.7.6	15	18	182.806258	153.025828	43.948344	2.885202e-54
LF.7.3	54	18	178.114496	160.596294	28.807413	5.594812e-51

Target sequence

, 241_C|T, 313_C|T, 670_T|G, 897_C|A, 934_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4584_A|G, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 15763_C|T, 16376_C|T, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22001_A|G, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A,
23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T,
26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29734_29759

 Case 58 (XFG): USA/NY-PRL-250520_81F07/2025



Target: 530 samples        Number of changes: 155                                               
BC: KS.1.3 + XFG.3         BC BR: 4-5                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-4,9-155 Gap history (edge excluded): 4-9
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 2.00e-214 Rec. model vs L2: 1.13e-08                                           
Flags: Model_2BP_Bad_L1_opp

KS.1.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KS.1.3	45	4	10.286720	NaN	NaN	NaN	*	*	*
KP.3.1	1957	8	8.879327	4.771811	-1.543623	0.004026	*
KP.3.2.9	28	4	8.768748	8.768748	-9.537496	0.219808	*	*
LK.2.1	10	4	8.699755	8.699755	-9.399510	0.204948	*	*
PR.2	20	4	8.648462	8.648462	-9.296923	0.194952	*	*
KR.1.1	33	4	8.541924	8.541924	-9.083849	0.174645	*	*
JN.2.5	25	4	8.435789	8.435789	-8.871579	0.157237	*	*
KP.2.15	253	4	8.319432	8.319432	-8.638864	0.140156	*	*
JN.1.16.5	24	4	7.781727	7.781727	-7.563453	0.081676	*	*
LF.7.3.1	26	4	7.705023	7.705023	-7.410046	0.075774	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	9	285.079706	NaN	NaN	NaN	*	*	*
LF.7	58	9	257.824674	238.888377	-127.776754	5.634715e-17		*
XFG.2	500	9	255.322126	238.966995	-127.933989	6.073570e-17		*
XFG.3.1	87	18	238.660957	219.640359	-89.280718	2.458687e-25
XFG.1	14	18	223.954846	203.714357	-57.428715	2.982384e-32
LF.7.1.8	44	18	204.917733	169.409944	11.180111	3.767830e-47
LF.7.7.1	188	18	203.503019	164.881084	20.237832	4.061976e-49
LF.7.1	165	18	185.740514	150.254780	49.490440	1.807926e-55
LF.7.6	15	18	182.806258	153.025828	43.948344	2.885202e-54
LF.7.3	54	18	178.114496	160.596294	28.807413	5.594812e-51

Target sequence

 Case 58 (XFG): USA/NY-PRL-250708_81D01/2025



Target: 530 samples         Number of changes: 155                                                          
BC: XFG.3 + KP.3.1.5 + XFG.3 BC BR: 3-4, 7-8                   BC BR coord: 896 - 897, 3430 - 3431    
Direction L1: <<            Initial region span: 1-3,5-7,8-155 Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []                                                                                            
Model 1BP/2BP comparison:   2BP vs 1BP: 6.82e-02                                                                   
Rec. model vs L1: 5.55e-09  Rec. model vs L2: 3.08e-218                                                     
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	3	4.704173	None	None	None	*	*	*

|||||

KP.3.1.5 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.5	45	5	7.613984	NaN	NaN	NaN	*	*	*
XBB.2.3.14	18	5	7.613984	-2.386016	22.772033	1.000000e+00	*	*
NL.11	57	5	7.208518	-2.791482	23.582963	6.669768e-01	*	*
XBB.4	49	4	6.609415	6.609415	4.781171	8.062670e+03	*	*
B.1.1.304	143	6	6.536776	-19.539319	57.078638	3.545505e-08		*
AZ.5	21	6	6.536776	-23.368480	64.736960	7.697156e-10		*
B.1.1.434	1274	6	6.534418	-27.588067	73.176135	1.131378e-11		*
XBB.1.5.92	41	4	6.272764	6.272764	5.454472	5.767535e+03	*	*
JE.1.1.1	46	5	5.577102	-11.675249	41.350497	9.234306e-05	*	*
LE.1.2	19	5	5.362692	-12.680191	43.360383	3.380168e-05	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	8	272.723168	NaN	NaN	NaN	*	*	*
LF.7	58	8	262.666982	267.385801	-184.771602	4.361977e-05	*	*
XFG.2	500	8	245.322126	250.010745	-150.021491	1.241129e-12		*
XFG.3.1	87	8	228.559265	233.278084	-116.556168	6.730853e-20		*
XFG.1	14	8	212.633263	217.352082	-84.704165	8.123796e-27		*
LF.7.1.8	44	16	184.917733	182.978160	-15.956320	9.617399e-42
LF.7.1	165	16	165.740514	163.861961	22.276079	4.779111e-50
LF.7.7.1	188	34	163.425568	156.919941	36.160117	4.627468e-53
LF.7.1.2	26	16	161.575508	159.673523	30.652954	7.274862e-52
LF.7.1.5	40	16	151.940084	150.116541	49.766919	5.128254e-56

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2485_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 9598_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12754_C|T, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19593_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23373_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27754_G|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29734_29759

 Case 58 (XFG): USA/NY-PRL-250708_81F10/2025



Target: 530 samples        Number of changes: 151                                               
BC: LD.1 + XFG.3           BC BR: 4-5                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-4,6-151 Gap history (edge excluded): 4-6
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 2.19e-197 Rec. model vs L2: 1.33e-07                                           
Flags: Model_2BP_Bad_L1_opp

LD.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LD.1	70	4	9.085704	NaN	NaN	NaN	*	*	*
XEC.29	135	4	8.457912	8.457912	-8.915824	0.535261	*	*
BA.5.1.17	357	3	8.456578	-1.543422	11.086845	0.000024	*	*
JN.1.29	69	4	7.971640	7.971640	-7.943281	0.327915	*	*
KP.2	1589	5	7.815486	6.243829	-4.487657	0.058426	*	*
MC.8	93	4	7.731975	7.731975	-7.463950	0.257947	*	*
XEC.39	155	4	7.208205	7.208205	-6.416409	0.153355	*	*
MC.9	298	4	6.547233	6.547233	-5.094467	0.078866	*	*
MC.2	396	4	6.252566	6.252566	-4.505133	0.059013	*	*
MC.1	932	4	6.073660	6.073660	-4.147321	0.049292	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	6	292.228759	NaN	NaN	NaN	*	*	*
LF.7	58	6	288.888377	278.888377	-215.776754	3.543696e-02	*	*
XFG.2	500	6	277.620087	269.918994	-197.837988	4.506454e-06		*
XFG.3.1	87	6	269.640359	259.640359	-177.280718	1.546278e-10		*
XFG.1	14	6	253.714357	243.714357	-145.428715	1.875634e-17		*
LF.7.7.1	188	14	211.719025	183.341668	-24.683335	1.128804e-43
LF.7.1	165	14	209.808982	201.200980	-60.401960	6.443445e-36
LF.7.1.8	44	14	201.708175	182.172322	-22.344644	3.503436e-44
LF.7.6	15	14	198.460035	178.924182	-15.848364	1.365239e-45
LF.7.3	54	14	195.118331	175.506628	-9.013256	4.466028e-47

Target sequence

, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T,
22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T,
25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26749_T|C, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28010_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29137_C|T, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/NY-PRL-250708_81F10/2025



Target: 530 samples        Number of changes: 151                                               
BC: LD.1 + XFG.3           BC BR: 4-5                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-4,6-151 Gap history (edge excluded): 4-6
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 2.19e-197 Rec. model vs L2: 1.33e-07                                           
Flags: Model_2BP_Bad_L1_opp

LD.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LD.1	70	4	9.085704	NaN	NaN	NaN	*	*	*
XEC.29	135	4	8.457912	8.457912	-8.915824	0.535261	*	*
BA.5.1.17	357	3	8.456578	-1.543422	11.086845	0.000024	*	*
JN.1.29	69	4	7.971640	7.971640	-7.943281	0.327915	*	*
KP.2	1589	5	7.815486	6.243829	-4.487657	0.058426	*	*
MC.8	93	4	7.731975	7.731975	-7.463950	0.257947	*	*
XEC.39	155	4	7.208205	7.208205	-6.416409	0.153355	*	*
MC.9	298	4	6.547233	6.547233	-5.094467	0.078866	*	*
MC.2	396	4	6.252566	6.252566	-4.505133	0.059013	*	*
MC.1	932	4	6.073660	6.073660	-4.147321	0.049292	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	6	292.228759	NaN	NaN	NaN	*	*	*
LF.7	58	6	288.888377	278.888377	-215.776754	3.543696e-02	*	*
XFG.2	500	6	277.620087	269.918994	-197.837988	4.506454e-06		*
XFG.3.1	87	6	269.640359	259.640359	-177.280718	1.546278e-10		*
XFG.1	14	6	253.714357	243.714357	-145.428715	1.875634e-17		*
LF.7.7.1	188	14	211.719025	183.341668	-24.683335	1.128804e-43
LF.7.1	165	14	209.808982	201.200980	-60.401960	6.443445e-36
LF.7.1.8	44	14	201.708175	182.172322	-22.344644	3.503436e-44
LF.7.6	15	14	198.460035	178.924182	-15.848364	1.365239e-45
LF.7.3	54	14	195.118331	175.506628	-9.013256	4.466028e-47

Target sequence

 Case 58 (XFG): USA/NY-PRL-250715_81G02/2025



Target: 530 samples       Number of changes: 153                                                          
BC: LF.7 + KP.3.1.5 + LF.7 BC BR: 4-5, 7-8                   BC BR coord: 2487 - 2488, 3430 - 3431  
Direction L1: <<          Initial region span: 1-3,5-7,8-153 Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []                                                                                          
Model 1BP/2BP comparison: 2BP vs 1BP: 6.72e-02                                                                   
Rec. model vs L1: 5.52e-09 Rec. model vs L2: 2.84e-220                                                     
Flags: Model_2BP_Best

LF.7 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	3	4.718819	None	None	None	*	*	*

|||||

KP.3.1.5 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.5	45	5	7.613984	NaN	NaN	NaN	*	*	*
XBB.2.3.14	18	5	7.613984	7.613984	-7.227967	1.000000	*	*
NL.11	57	5	7.208518	7.208518	-6.417037	0.666977	*	*
XBB.4	49	4	6.609415	3.722163	0.555673	0.020343	*	*
B.1.1.304	143	6	6.536776	-3.463224	14.926449	0.000015	*	*
AZ.5	21	6	6.536776	-3.463224	14.926449	0.000015	*	*
B.1.1.434	1274	6	6.534418	-3.465582	14.931164	0.000015	*	*
XBB.1.5.92	41	4	6.272764	3.900411	0.199177	0.024355	*	*
JE.1.1.1	46	5	5.577102	5.577102	-3.154203	0.130029	*	*
LE.1.2	19	5	5.362692	-2.680191	13.360383	0.000034	*	*

|||||

LF.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	8	282.666982	NaN	NaN	NaN	*	*	*
XFG.3	480	8	281.735746	276.439919	-204.879838	3.886796e-01	*	*
XFG.2	500	8	265.322126	260.010745	-172.021491	2.845335e-08		*
XFG.3.1	87	8	248.559265	243.278084	-138.556168	1.543074e-15		*
XFG.1	14	8	232.633263	227.352082	-106.704165	1.862411e-22		*
LF.7.1.8	44	16	204.917733	192.978160	-37.956320	2.204826e-37
LF.7.1	165	16	185.740514	173.861961	0.276079	1.095630e-45
LF.7.7.1	188	12	182.783973	166.919941	14.160117	1.060865e-48
LF.7.1.2	26	16	181.575508	169.673523	8.652954	1.667790e-47
LF.7.1.5	40	16	171.940084	160.116541	27.766919	1.175672e-51

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2485_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19593_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23373_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27754_G|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/NY-PRL-250715_81G02/2025



Target: 530 samples       Number of changes: 153                                                          
BC: LF.7 + KP.3.1.5 + LF.7 BC BR: 4-5, 7-8                   BC BR coord: 2487 - 2488, 3430 - 3431  
Direction L1: <<          Initial region span: 1-3,5-7,8-153 Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []                                                                                          
Model 1BP/2BP comparison: 2BP vs 1BP: 6.72e-02                                                                   
Rec. model vs L1: 5.52e-09 Rec. model vs L2: 2.84e-220                                                     
Flags: Model_2BP_Best

LF.7 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	3	4.718819	None	None	None	*	*	*

|||||

KP.3.1.5 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.5	45	5	7.613984	NaN	NaN	NaN	*	*	*
XBB.2.3.14	18	5	7.613984	7.613984	-7.227967	1.000000	*	*
NL.11	57	5	7.208518	7.208518	-6.417037	0.666977	*	*
XBB.4	49	4	6.609415	3.722163	0.555673	0.020343	*	*
B.1.1.304	143	6	6.536776	-3.463224	14.926449	0.000015	*	*
AZ.5	21	6	6.536776	-3.463224	14.926449	0.000015	*	*
B.1.1.434	1274	6	6.534418	-3.465582	14.931164	0.000015	*	*
XBB.1.5.92	41	4	6.272764	3.900411	0.199177	0.024355	*	*
JE.1.1.1	46	5	5.577102	5.577102	-3.154203	0.130029	*	*
LE.1.2	19	5	5.362692	-2.680191	13.360383	0.000034	*	*

|||||

LF.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	8	282.666982	NaN	NaN	NaN	*	*	*
XFG.3	480	8	281.735746	276.439919	-204.879838	3.886796e-01	*	*
XFG.2	500	8	265.322126	260.010745	-172.021491	2.845335e-08		*
XFG.3.1	87	8	248.559265	243.278084	-138.556168	1.543074e-15		*
XFG.1	14	8	232.633263	227.352082	-106.704165	1.862411e-22		*
LF.7.1.8	44	16	204.917733	192.978160	-37.956320	2.204826e-37
LF.7.1	165	16	185.740514	173.861961	0.276079	1.095630e-45
LF.7.7.1	188	12	182.783973	166.919941	14.160117	1.060865e-48
LF.7.1.2	26	16	181.575508	169.673523	8.652954	1.667790e-47
LF.7.1.5	40	16	171.940084	160.116541	27.766919	1.175672e-51

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2485_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19593_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23373_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27754_G|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/NY-PRL-250722_81C08/2025



Target: 530 samples        Number of changes: 157                                               
BC: KS.1.3 + XFG.3         BC BR: 4-5                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-4,9-157 Gap history (edge excluded): 4-9
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 9.02e-222 Rec. model vs L2: 1.13e-08                                           
Flags: Model_2BP_Bad_L1_opp

KS.1.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KS.1.3	45	4	10.286720	NaN	NaN	NaN	*	*	*
KP.3.1	1957	8	8.879327	4.771811	-1.543623	0.004026	*
KP.3.2.9	28	4	8.768748	8.768748	-9.537496	0.219808	*	*
LK.2.1	10	4	8.699755	8.699755	-9.399510	0.204948	*	*
PR.2	20	4	8.648462	8.648462	-9.296923	0.194952	*	*
KR.1.1	33	4	8.541924	8.541924	-9.083849	0.174645	*	*
JN.2.5	25	4	8.435789	8.435789	-8.871579	0.157237	*	*
KP.2.15	253	4	8.319432	8.319432	-8.638864	0.140156	*	*
JN.1.16.5	24	4	7.781727	7.781727	-7.563453	0.081676	*	*
LF.7.3.1	26	4	7.705023	7.705023	-7.410046	0.075774	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	9	279.302040	NaN	NaN	NaN	*	*	*
XFG.2	500	9	247.105743	230.750611	-107.501222	5.320311e-18		*
LF.7	58	9	237.824674	218.888377	-83.776754	3.760144e-23		*
XFG.3.1	87	18	218.660957	199.640359	-45.280718	1.640724e-31
XFG.1	14	18	203.954846	183.714357	-13.428715	1.990197e-38
LF.7.1.8	44	18	198.438621	162.930832	28.138336	1.871049e-47
LF.7.7.1	188	18	197.651096	159.029161	35.941678	3.787361e-49
LF.7.1	165	18	180.136870	144.651137	64.697727	2.153685e-55
LF.7.6	15	18	162.806258	133.025828	87.948344	1.925346e-60
LF.7.1.2	26	18	162.320821	126.781111	100.437778	3.735422e-63

Target sequence

, 241_C|T, 313_C|T, 670_T|G, 897_C|A, 934_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4584_A|G, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 15763_C|T, 16376_C|T, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20825_C|T, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22001_A|G, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T,
22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23601_C|T,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T,
26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A,
29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/NY-PRL-250722_81F09/2025



Target: 530 samples        Number of changes: 152                                               
BC: LD.1 + XFG.3           BC BR: 4-5                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-4,6-152 Gap history (edge excluded): 4-6
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 2.19e-197 Rec. model vs L2: 1.33e-07                                           
Flags: Model_2BP_Bad_L1_opp

LD.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LD.1	70	4	9.085704	NaN	NaN	NaN	*	*	*
XEC.29	135	4	8.457912	8.457912	-8.915824	0.535261	*	*
BA.5.1.17	357	3	8.456578	-1.543422	11.086845	0.000024	*	*
JN.1.29	69	4	7.971640	7.971640	-7.943281	0.327915	*	*
KP.2	1589	5	7.815486	6.243829	-4.487657	0.058426	*	*
MC.8	93	4	7.731975	7.731975	-7.463950	0.257947	*	*
XEC.39	155	4	7.208205	7.208205	-6.416409	0.153355	*	*
MC.9	298	4	6.547233	6.547233	-5.094467	0.078866	*	*
MC.2	396	4	6.252566	6.252566	-4.505133	0.059013	*	*
MC.1	932	4	6.073660	6.073660	-4.147321	0.049292	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	6	282.228759	NaN	NaN	NaN	*	*	*
LF.7	58	6	278.888377	268.888377	-193.776754	3.543696e-02	*	*
XFG.2	500	6	267.620087	259.918994	-175.837988	4.506454e-06		*
XFG.3.1	87	6	259.640359	249.640359	-155.280718	1.546278e-10		*
XFG.1	14	6	243.714357	233.714357	-123.428715	1.875634e-17		*
LF.7.7.1	188	14	201.719025	173.341668	-2.683335	1.128804e-43
LF.7.1	165	14	199.808982	191.200980	-38.401960	6.443445e-36
LF.7.1.8	44	14	191.708175	172.172322	-0.344644	3.503436e-44
LF.7.6	15	14	188.460035	168.924182	6.151636	1.365239e-45
LF.7.3	54	14	185.118331	165.506628	12.986744	4.466028e-47

Target sequence

, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15327_G|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C,
21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T,
25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26749_T|C, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28010_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29137_C|T, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/NY-PRL-250728_81D05/2025



Target: 530 samples         Number of changes: 154                                                          
BC: XFG.3 + KP.3.1.5 + XFG.3 BC BR: 3-4, 7-8                   BC BR coord: 896 - 897, 3430 - 3431    
Direction L1: <<            Initial region span: 1-3,5-7,8-154 Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []                                                                                            
Model 1BP/2BP comparison:   2BP vs 1BP: 6.82e-02                                                                   
Rec. model vs L1: 5.55e-09  Rec. model vs L2: 3.30e-201                                                     
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	3	4.704173	None	None	None	*	*	*

|||||

KP.3.1.5 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.5	45	5	7.613984	NaN	NaN	NaN	*	*	*
XBB.2.3.14	18	5	7.613984	-2.386016	22.772033	1.000000e+00	*	*
NL.11	57	5	7.208518	-2.791482	23.582963	6.669768e-01	*	*
XBB.4	49	4	6.609415	6.609415	4.781171	8.062670e+03	*	*
B.1.1.304	143	6	6.536776	-19.539319	57.078638	3.545505e-08		*
AZ.5	21	6	6.536776	-23.368480	64.736960	7.697156e-10		*
B.1.1.434	1274	6	6.534418	-27.588067	73.176135	1.131378e-11		*
XBB.1.5.92	41	4	6.272764	6.272764	5.454472	5.767535e+03	*	*
JE.1.1.1	46	5	5.577102	-11.675249	41.350497	9.234306e-05	*	*
LE.1.2	19	5	5.362692	-12.680191	43.360383	3.380168e-05	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	8	232.800723	NaN	NaN	NaN	*	*	*
LF.7	58	8	219.299864	224.018683	-86.037366	1.391678e-06		*
XFG.2	500	8	206.201918	210.890537	-59.781074	2.762182e-12		*
XFG.3.1	87	8	204.183727	208.902547	-55.805093	3.794703e-13		*
XFG.1	14	8	142.417961	147.136780	67.726439	5.659886e-40		*
LF.7.1.8	44	16	140.641999	138.702426	84.595149	1.228949e-43
LF.7.1	165	16	123.055570	121.177017	119.645967	3.009698e-51
LF.7.7.1	188	34	121.195120	114.689494	132.621012	4.593283e-54
LF.7.3.1	26	16	113.050269	115.717675	130.564651	1.286609e-53
LF.7.1.5	40	54	111.611145	79.901239	202.197523	3.572878e-69

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2485_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 9598_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12754_C|T, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16064_A|G, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19593_C|T, 19955_C|T, 20055_A|G, 21610_T|C, 21641_G|T,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23373_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24769_T|C, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27754_G|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/NY-PRL-250728_81H09/2025



Target: 530 samples           Number of changes: 148                                                                          
BC: XFG.3 + XBB.1.42.1 + XFG.3 BC BR: 135-136, 140-141                   BC BR coord: 27808 - 27809, 28361 - 28362      
Direction L1: >>              Initial region span: 1-135,137-140,141-148 Gap history (edge excluded): 135-141 -> 135-137
Alt. candidates: [], []                                                                                                              
Model 1BP/2BP comparison:     2BP vs 1BP: 1.00e-06                                                                                   
Rec. model vs L1: 1.26e-07    Rec. model vs L2: 0.00e+00                                                                      
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	135	265.894236	NaN	NaN	NaN	*	*	*
LF.7	58	135	252.901546	264.770108	-189.540216	2.155657e-07		*
XFG.3.1	87	135	251.650859	265.211030	-190.422060	3.347105e-07		*
XFG.2	500	135	249.547299	263.886110	-187.772220	8.896703e-08		*
LF.7.1.8	44	135	194.127090	192.391476	-44.782951	7.931313e-39		*
XFG.1	14	135	174.651239	189.115097	-38.230193	2.999374e-40		*
LF.7.1	165	135	163.846563	173.779337	-7.558674	6.563338e-47		*
LF.7.7.1	188	147	161.559857	164.299140	11.401720	5.012024e-51
LF.7.3.1	26	135	159.503538	157.695991	24.608018	6.784191e-54		*
LF.7.3	54	135	149.789073	148.170299	43.659403	4.952712e-58		*

|||||

XBB.1.42.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XBB.1.42.1	91	137	10.168975	NaN	NaN	NaN	*	*	*
LF.7.6.1	26	137	10.035444	-13.338585	42.677171	0.000035	*	*
FL.1.3	49	137	9.401720	-3.850097	23.700193	0.458406	*	*
LF.7.7.1	188	137	8.057099	-5.557252	27.114504	0.083326	*	*
FL.15.1.1	198	137	8.005274	-5.246543	26.493087	0.113608	*	*
HF.1.1	292	137	7.616787	-5.635030	27.270060	0.076919	*	*
EG.5.2	295	137	7.606565	-5.645252	27.290503	0.076154	*	*
NB.1.8.1	357	137	7.415805	-6.198546	28.397091	0.043718	*	*
EG.6.1	838	137	7.255670	-5.993758	27.987515	0.053665	*	*
XBB.1.9.1	1695	137	7.235525	-6.012746	28.025492	0.052602	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	141	14.226904	None	None	None	*	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2698_T|C, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10039_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10744_T|C, 11042_G|T, 11288_11296, 11727_G|A, 12459_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21610_T|C, 21641_G|T, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A,
23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23487_T|G, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|A, 28271_A|T, 28297_T|C,
28311_C|T, 28340_T|C, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/NY-PRL-250728_82B06/2025



Target: 530 samples         Number of changes: 153                                                          
BC: XFG.3 + KP.3.1.5 + XFG.3 BC BR: 3-4, 7-8                   BC BR coord: 896 - 897, 3430 - 3431    
Direction L1: <<            Initial region span: 1-3,5-7,8-153 Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []                                                                                            
Model 1BP/2BP comparison:   2BP vs 1BP: 6.82e-02                                                                   
Rec. model vs L1: 5.55e-09  Rec. model vs L2: 3.30e-201                                                     
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	3	4.704173	None	None	None	*	*	*

|||||

KP.3.1.5 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.5	45	5	7.613984	NaN	NaN	NaN	*	*	*
XBB.2.3.14	18	5	7.613984	-2.386016	22.772033	1.000000e+00	*	*
NL.11	57	5	7.208518	-2.791482	23.582963	6.669768e-01	*	*
XBB.4	49	4	6.609415	6.609415	4.781171	8.062670e+03	*	*
B.1.1.304	143	6	6.536776	-19.539319	57.078638	3.545505e-08		*
AZ.5	21	6	6.536776	-23.368480	64.736960	7.697156e-10		*
B.1.1.434	1274	6	6.534418	-27.588067	73.176135	1.131378e-11		*
XBB.1.5.92	41	4	6.272764	6.272764	5.454472	5.767535e+03	*	*
JE.1.1.1	46	5	5.577102	-11.675249	41.350497	9.234306e-05	*	*
LE.1.2	19	5	5.362692	-12.680191	43.360383	3.380168e-05	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	8	242.800723	NaN	NaN	NaN	*	*	*
LF.7	58	8	229.299864	234.018683	-106.037366	1.391678e-06		*
XFG.2	500	8	216.201918	220.890537	-79.781074	2.762182e-12		*
XFG.3.1	87	8	214.183727	218.902547	-75.805093	3.794703e-13		*
XFG.1	14	8	152.417961	157.136780	47.726439	5.659886e-40		*
LF.7.1.8	44	16	150.641999	148.702426	64.595149	1.228949e-43
LF.7.1	165	16	133.055570	131.177017	99.645967	3.009698e-51
LF.7.7.1	188	34	131.195120	124.689494	112.621012	4.593283e-54
LF.7.3.1	26	16	123.050269	125.717675	110.564651	1.286609e-53
LF.7.7.2	239	12	114.883598	109.063369	143.873263	7.520937e-61

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2485_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 9598_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12754_C|T, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19593_C|T, 19955_C|T, 20055_A|G, 21610_T|C, 21641_G|T, 21653_T|C,
21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G,
23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23373_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27754_G|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28857_G|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/NY-PRL-250728_82C09/2025



Target: 530 samples         Number of changes: 150                                                          
BC: XFG.3 + KP.3.1.5 + XFG.3 BC BR: 3-4, 7-8                   BC BR coord: 896 - 897, 3430 - 3431    
Direction L1: <<            Initial region span: 1-3,5-7,8-150 Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []                                                                                            
Model 1BP/2BP comparison:   2BP vs 1BP: 6.82e-02                                                                   
Rec. model vs L1: 5.55e-09  Rec. model vs L2: 3.33e-195                                                     
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	3	4.704173	None	None	None	*	*	*

|||||

KP.3.1.5 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.5	45	5	7.613984	NaN	NaN	NaN	*	*	*
XBB.2.3.14	18	5	7.613984	-2.386016	22.772033	1.000000e+00	*	*
NL.11	57	5	7.208518	-2.791482	23.582963	6.669768e-01	*	*
XBB.4	49	4	6.609415	6.609415	4.781171	8.062670e+03	*	*
B.1.1.304	143	6	6.536776	-19.539319	57.078638	3.545505e-08		*
AZ.5	21	6	6.536776	-23.368480	64.736960	7.697156e-10		*
B.1.1.434	1274	6	6.534418	-27.588067	73.176135	1.131378e-11		*
XBB.1.5.92	41	4	6.272764	6.272764	5.454472	5.767535e+03	*	*
JE.1.1.1	46	5	5.577102	-11.675249	41.350497	9.234306e-05	*	*
LE.1.2	19	5	5.362692	-12.680191	43.360383	3.380168e-05	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	8	261.813302	NaN	NaN	NaN	*	*	*
LF.7	58	8	259.299864	264.018683	-172.037366	8.249645e-02	*	*
XFG.2	500	8	246.201918	250.890537	-145.781074	1.637377e-07		*
XFG.3.1	87	8	244.183727	248.902547	-141.805093	2.249439e-08		*
XFG.1	14	8	182.417961	187.136780	-18.273561	3.355089e-35		*
LF.7.1.8	44	16	180.641999	178.702426	-1.404851	7.285009e-39
LF.7.1	165	16	163.055570	161.177017	33.645967	1.784100e-46
LF.7.7.1	188	12	160.553525	154.689494	46.621012	2.722824e-49
LF.7.3.1	26	16	153.050269	155.717675	44.564651	7.626809e-49
LF.7.7.2	239	12	144.883598	139.063369	77.873263	4.458290e-56

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2485_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19593_C|T, 19955_C|T, 20055_A|G, 21610_T|C, 21641_G|T, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C,
23222_G|A, 23271_C|T, 23277_C|T, 23373_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T,
25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27754_G|C, 27807_C|T,
27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/NY-PRL-250728_82D06/2025



Target: 530 samples        Number of changes: 149                                                                          
BC: XFG.3 + XDD.1.1 + XFG.3 BC BR: 136-137, 142-143                   BC BR coord: 27915 - 27916, 28880 - 28881      
Direction L1: >>           Initial region span: 1-136,138-142,143-149 Gap history (edge excluded): 136-143 -> 136-138
Alt. candidates: [], []                                                                                                           
Model 1BP/2BP comparison:  2BP vs 1BP: 1.15e-07                                                                                   
Rec. model vs L1: 1.58e-07 Rec. model vs L2: 5.93e-323                                                                     
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	136	258.237613	NaN	NaN	NaN	*	*	*
LF.7	58	136	256.515897	267.640847	-195.281693	1.592285e-02	*	*
XFG.2	500	136	253.161649	266.725765	-193.451530	6.377367e-03	*	*
XFG.3.1	87	136	240.935043	253.891959	-167.783917	1.700089e-08		*
XFG.1	14	136	178.265589	191.950744	-43.901488	2.139299e-35		*
LF.7.1.8	44	136	170.738844	168.224526	3.550948	1.063249e-45		*
LF.7.1	165	136	167.460914	176.639525	-13.279050	4.799798e-42		*
LF.7.3.1	26	136	163.117889	160.654240	18.691519	5.483094e-49		*
LF.7.7.1	188	136	162.823905	167.134787	5.730425	3.574818e-46		*
LF.7.3	54	136	153.403424	151.024638	37.950724	3.603876e-53		*

|||||

XDD.1.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XDD.1.1	29	138	13.385163	NaN	NaN	NaN	*	*	*
JG.3	1482	138	10.138247	0.138247	17.723506	3.896856e-02	*	*
HK.3	1830	138	9.256169	-0.743831	19.487662	1.608288e-02	*	*
JN.1.3	111	140	8.464940	-16.336019	50.672039	2.727174e-09
XBB.1.5.43	48	140	8.201786	-11.033084	40.066167	5.463533e-07
GK.2.1	255	138	7.855661	-8.235089	34.470179	8.984587e-06		*
BW.1	131	140	7.218843	-12.016026	42.032053	2.050525e-07
XBB.1.16.6	4784	137	6.553074	6.553074	4.893853	2.380748e+01	*	*
BA.2.76	427	140	6.030217	-13.204653	44.409305	6.238132e-08
BA.2.36	3016	140	5.869129	-13.366736	44.733472	5.315785e-08

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	143	13.542054	None	None	None	*	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4822_A|G, 5239_C|T, 6183_A|G, 6351_A|G, 6777_A|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 9989_A|G, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 16986_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21610_T|C, 21641_G|T, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28268_A|C,
28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28467_A|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/OSPHL10334/2025



Target: 530 samples        Number of changes: 148                                           
BC: EG.5.1.16 + XFG.3      BC BR: 5-6                    BC BR coord: 2512 - 2513    
Direction L1: <<           Initial region span: 1-5,6-148 Gap history (edge excluded):
Alt. candidates: [], []                                                                            
Model 1BP/2BP comparison:  -                                                                       
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 9.53e-23                                       
Flags: Model_2BP_Bad_L1_opp

EG.5.1.16 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
EG.5.1.16	519	5	6.229741	NaN	NaN	NaN	*	*	*
EG.5.2	295	5	6.214795	6.214795	5.570409	9.851119e-01	*	*
HK.27.1	107	4	5.873577	-4.126423	26.252847	3.183323e-05	*	*
JN.11	67	3	5.085550	-18.541804	55.083609	1.747937e-11
KP.2.3.10	10	3	4.790433	-18.836921	55.673843	1.301394e-11
HK.29	238	4	4.691106	-5.308894	28.617788	9.732887e-06		*
DN.3	10	3	4.685073	-18.767248	55.534496	1.395756e-11
BF.5.5	91	3	4.661600	-18.338270	54.676541	2.134935e-11
PL.1.1	12	3	4.608112	-19.019243	56.038486	1.081594e-11
BN.1.1.1	41	3	4.453366	-15.546634	49.093268	3.493314e-10

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	6	333.613273	NaN	NaN	NaN	*	*	*
LF.7	58	6	333.571870	333.571870	-335.143740	9.559975e-01	*	*
XFG.2	500	5	329.187907	328.801106	-325.602212	8.107222e-03	*	*
XFG.3.1	87	6	301.566276	301.566276	-271.132551	1.204653e-14		*
XFG.1	14	6	284.571728	284.571728	-237.143455	5.012185e-22		*
LF.7.1	165	12	242.566038	241.941555	-151.883111	1.534806e-40
LF.7.7.1	188	12	238.986556	229.544250	-127.088501	6.352918e-46
LF.7.1.8	44	12	235.721266	235.115133	-138.230265	1.667222e-43
LF.7.6	15	12	220.487112	219.880978	-107.761956	4.031968e-50
LF.7.3	54	12	217.040048	216.358064	-100.716127	1.193440e-51

Target sequence

, 241_C|T, 670_T|G, 683_C|T, 2334_C|T, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G,
22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

 Case 58 (XFG): USA/NY-PRL-250715_81G02/2025



Target: 530 samples       Number of changes: 153                                                          
BC: LF.7 + KP.3.1.5 + LF.7 BC BR: 4-5, 7-8                   BC BR coord: 2487 - 2488, 3430 - 3431  
Direction L1: <<          Initial region span: 1-3,5-7,8-153 Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []                                                                                          
Model 1BP/2BP comparison: 2BP vs 1BP: 6.72e-02                                                                   
Rec. model vs L1: 5.52e-09 Rec. model vs L2: 2.84e-220                                                     
Flags: Model_2BP_Best

LF.7 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	3	4.718819	None	None	None	*	*	*

|||||

KP.3.1.5 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.5	45	5	7.613984	NaN	NaN	NaN	*	*	*
XBB.2.3.14	18	5	7.613984	7.613984	-7.227967	1.000000	*	*
NL.11	57	5	7.208518	7.208518	-6.417037	0.666977	*	*
XBB.4	49	4	6.609415	3.722163	0.555673	0.020343	*	*
B.1.1.304	143	6	6.536776	-3.463224	14.926449	0.000015	*	*
AZ.5	21	6	6.536776	-3.463224	14.926449	0.000015	*	*
B.1.1.434	1274	6	6.534418	-3.465582	14.931164	0.000015	*	*
XBB.1.5.92	41	4	6.272764	3.900411	0.199177	0.024355	*	*
JE.1.1.1	46	5	5.577102	5.577102	-3.154203	0.130029	*	*
LE.1.2	19	5	5.362692	-2.680191	13.360383	0.000034	*	*

|||||

LF.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	8	282.666982	NaN	NaN	NaN	*	*	*
XFG.3	480	8	281.735746	276.439919	-204.879838	3.886796e-01	*	*
XFG.2	500	8	265.322126	260.010745	-172.021491	2.845335e-08		*
XFG.3.1	87	8	248.559265	243.278084	-138.556168	1.543074e-15		*
XFG.1	14	8	232.633263	227.352082	-106.704165	1.862411e-22		*
LF.7.1.8	44	16	204.917733	192.978160	-37.956320	2.204826e-37
LF.7.1	165	16	185.740514	173.861961	0.276079	1.095630e-45
LF.7.7.1	188	12	182.783973	166.919941	14.160117	1.060865e-48
LF.7.1.2	26	16	181.575508	169.673523	8.652954	1.667790e-47
LF.7.1.5	40	16	171.940084	160.116541	27.766919	1.175672e-51

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2485_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19593_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23373_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27754_G|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): USA/VT-25-006305-WGS-01/2025



Target: 530 samples        Number of changes: 148                                           
BC: MC.20 + XFG.3          BC BR: 3-4                    BC BR coord: 865 - 866      
Direction L1: <<           Initial region span: 1-3,4-148 Gap history (edge excluded):
Alt. candidates: [], []                                                                            
Model 1BP/2BP comparison:  -                                                                       
Rec. model vs L1: 4.28e-230 Rec. model vs L2: 5.60e-09                                       
Flags: Model_2BP_Bad_L1_opp

MC.20 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.20	14	3	8.387412	NaN	NaN	NaN	*	*	*
BA.5.2.28	894	3	6.014678	6.014678	-4.029355	0.093481	*	*
CQ.2	434	3	5.942716	5.942716	-3.885432	0.087161	*	*
BA.5.2.12	97	3	5.758611	5.758611	-3.517223	0.072440	*	*
XEC.2.1	265	3	5.572695	5.572695	-3.145391	0.060205	*	*
PA.1.3	18	3	5.497040	5.497040	-2.994081	0.055576	*	*
GK.1.6	51	3	5.192024	5.192024	-2.384049	0.040967	*	*
JN.1.37	26	3	5.129316	5.129316	-2.258631	0.038581	*	*
HK.3.2	356	3	5.118018	5.118018	-2.236036	0.038197	*	*
MS.1	34	3	4.861052	4.861052	-1.722103	0.029452	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	4	280.901341	NaN	NaN	NaN	*	*	*
LF.7	58	4	280.213079	280.213079	-218.426158	5.040902e-01	*	*
XFG.2	500	16	275.212650	269.131672	-196.263343	7.733106e-06
XFG.3.1	87	4	247.532327	247.532327	-153.064655	3.218053e-15		*
XFG.1	14	16	232.793190	231.282640	-120.565280	2.834518e-22
LF.7.1.8	44	18	218.942307	195.673532	-49.347064	9.710750e-38
LF.7.1	165	18	211.647267	188.471569	-34.943139	7.213749e-41
LF.7.7.1	188	28	199.925659	170.882672	0.234656	1.663767e-48
LF.7.6	15	10	184.993709	180.691948	-19.383895	3.015435e-44
LF.7.1.2	26	18	182.863442	159.648486	22.703028	2.196818e-53

Target sequence

, 241_C|T, 670_T|G, 853_C|T, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6543_C|T, 7869_C|T, 8152_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10039_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15381_C|A, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C,
21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T,
25244_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): IGS-10285-CVDP-0E8038B3-F107-4098-A428-711708784AC4



Target: 530 samples        Number of changes: 151                                                       
BC: XFG.2 + KP.3.1.1       BC BR: 142-143                    BC BR coord: 28361 - 28362          
Direction L1: >>           Initial region span: 1-142,144-151 Gap history (edge excluded): 142-144
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 1.73e-06 Rec. model vs L2: 1.30e-141                                                  
Flags: Model_2BP_Bad_L1_opp

XFG.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.2	500	142	311.047405	NaN	NaN	NaN	*	*	*
LF.7	58	142	309.587062	309.587062	-295.174125	2.322363e-01	*	*
XFG.3	480	148	308.417909	307.128912	-290.257824	1.994055e-02	*
XFG.3.1	87	148	275.208799	273.919801	-223.839603	7.530388e-17
XFG.1	14	148	259.534111	258.245114	-192.490229	1.172874e-23
LF.7.1.8	44	142	224.571938	224.571938	-125.143877	2.782176e-38		*
LF.7.1	165	142	219.939926	219.939926	-115.879851	2.713946e-40		*
LF.7.6	15	142	216.244100	216.244100	-108.488200	6.743465e-42		*
LF.7.7.1	188	142	214.706097	214.706097	-105.412194	1.445671e-42		*
LF.7.3	54	142	206.001218	206.001218	-88.002436	2.396272e-46		*

|||||

KP.3.1.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.1	12013	144	9.673219	NaN	NaN	NaN	*	*	*
XBB.1.18.1	84	149	9.477560	-18.867943	65.735886	8.830979e-09
JN.1.46	308	149	7.040837	-7.696366	43.392731	6.298682e-04	*
BQ.1.1.13	384	149	6.727103	-25.186222	78.372445	1.597494e-11
DV.6	1051	149	5.873972	-22.486817	72.973635	2.377028e-10
JF.1.1	935	149	5.815039	-23.857788	75.715577	6.010068e-11
BF.5	7920	149	4.715060	-22.241819	72.483639	3.036942e-10
BF.7	11554	149	4.391464	-18.808267	65.616534	9.377056e-09
BA.2.9	75328	149	4.282623	-5.604268	39.208536	5.092431e-03	*
NL.14	12	144	3.685154	-6.314846	40.629691	2.503664e-03	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3912_C|A, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 5907_C|T, 6183_A|G, 7279_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G,
22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28467_A|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29436_A|G, 29510_A|C, 29734_29759

 Case 58 (XFG): IGS-10285-CVDP-34E9F1FA-26B3-4AD3-BB29-6A6F16FA356F



Target: 530 samples       Number of changes: 153                                                      
BC: XFG.3 + BY.1 + XFG.3  BC BR: 3-4, 6-7                   BC BR coord: 896 - 897, 2909 - 2910
Direction L1: <<          Initial region span: 1-3,4-6,7-153 Gap history (edge excluded): 3-7 ->
Alt. candidates: [], []                                                                                      
Model 1BP/2BP comparison: 2BP vs 1BP: 6.57e-07                                                               
Rec. model vs L1: 5.75e-15 Rec. model vs L2: 0.00e+00                                                  
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	3	4.704173	None	None	None	*	*	*

|||||

BY.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
BY.1	185	6	9.220286	NaN	NaN	NaN	*	*	*
EG.6.1.1	59	5	6.002246	-3.997754	17.995507	1.813957e-06		*
EG.6.1	838	5	5.981751	-4.018249	18.036497	1.778038e-06		*
BA.4.5	49	5	5.981627	-4.018373	18.036746	1.778038e-06		*
XFG.1	14	5	4.972627	-5.027373	20.054746	6.508413e-07		*
XCT.1	42	4	4.925038	-15.259019	40.518038	2.335991e-11
JG.4	61	4	4.925038	-15.225683	40.451365	2.419198e-11
B.1.258.16	10	4	4.925038	-15.074962	40.149923	2.810707e-11
AY.47	22935	4	4.917818	-15.082182	40.164364	2.796688e-11
XDK.1	127	5	4.745072	-5.254928	20.509857	5.171153e-07		*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	7	283.957599	NaN	NaN	NaN	*	*	*
LF.7	58	7	281.317960	286.036780	-224.073559	7.243976e-02	*	*
XFG.2	500	7	280.041205	284.729825	-221.459650	1.964367e-02	*	*
XFG.1	14	7	272.328306	277.047125	-206.094250	9.029622e-06		*
XFG.3.1	87	7	261.080690	265.799509	-183.599019	1.180397e-10		*
LF.7.7.1	188	12	196.168587	190.308442	-32.616884	1.937036e-43
LF.7.1	165	12	194.430741	197.417325	-46.834650	2.359391e-40
LF.7.1.8	44	12	186.068685	189.034653	-30.069306	5.412679e-44
LF.7.6	15	12	182.840632	185.876110	-23.752219	2.296369e-45
LF.7.7.2	239	12	180.400510	174.584167	-1.168335	2.869835e-50

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1684_C|T, 2790_C|T, 2904_T|C, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10868_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
13402_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16224_T|C, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20134_G|T, 20970_C|A, 21608_.|TCATGCCGCTGT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A,
23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 26951_G|C,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): IGS-10285-CVDP-6445BD5D-CEF7-4760-9DC3-A57A77560482



Target: 530 samples       Number of changes: 155                                                          
BC: XFG.3 + CV.1 + XFG.3  BC BR: 3-4, 7-8                   BC BR coord: 2474 - 2475, 3430 - 3431  
Direction L1: <<          Initial region span: 1-3,5-7,8-155 Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []                                                                                          
Model 1BP/2BP comparison: 2BP vs 1BP: 5.21e-02                                                                   
Rec. model vs L1: 5.55e-09 Rec. model vs L2: 0.00e+00                                                      
Flags: Model_2BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	3	4.704173	None	None	None	*	*	*

|||||

CV.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
CV.1	86	5	9.239404	NaN	NaN	NaN	*	*	*
BM.1.1.3	341	5	9.230568	-0.769432	11.538865	0.990050	*	*
BM.1.1.4	18	5	9.182246	-0.817754	11.635508	0.941765	*	*
NL.4	115	4	9.133467	9.133467	-8.266935	19830.967301	*	*
FL.29	37	5	7.014781	-2.985219	15.970439	0.108067	*	*
BA.5.6.1	96	5	6.977641	-3.022359	16.044718	0.104350	*	*
FY.5.2	12	5	6.754498	-3.245502	16.491005	0.083326	*	*
NA.1	15	5	6.531354	-3.468646	16.937292	0.066537	*	*
BQ.1.31	78	6	6.108072	-6.420323	22.840646	0.003483	*	*
EG.5.1.6	1581	5	6.047979	-3.952021	17.904043	0.041172	*	*

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	8	281.941538	NaN	NaN	NaN	*	*	*
XFG.2	500	8	262.481232	267.169851	-186.339703	3.484295e-09		*
LF.7	58	8	261.314074	266.032894	-184.065787	1.119930e-09		*
XFG.3.1	87	17	241.178496	245.795623	-143.591247	1.815810e-18
XFG.1	14	17	227.451939	230.849175	-113.698349	5.868666e-25
LF.7.1	165	17	189.291992	177.413439	-6.826878	3.647655e-48
LF.7.7.1	188	17	185.348216	170.304556	7.390889	2.979751e-51
LF.7.1.8	44	16	182.266109	180.326536	-12.653071	6.695927e-47
LF.7.6	15	17	172.014928	165.872223	16.255553	3.532514e-53
LF.7.1.2	26	17	171.151893	159.249908	29.500184	4.710364e-56

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2675_C|T, 2790_C|T, 3037_C|T, 3130_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6964_T|C, 7113_C|T, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14183_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18252_C|T, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22419_C|T, 22468_G|T, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28406_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29555_C|T, 29734_29759

 Case 58 (XFG): IGS-10285-CVDP-AECC2415-2C37-4298-B483-C570A97B84D9



Target: 530 samples        Number of changes: 152                                               
BC: JN.11 + LF.7           BC BR: 4-5                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-4,6-152 Gap history (edge excluded): 4-6
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 1.94e-228 Rec. model vs L2: 4.16e-08                                           
Flags: Model_2BP_Bad_L1_opp

JN.11 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.11	67	4	8.712905	NaN	NaN	NaN	*	*	*
KP.2.3.10	10	4	8.417788	8.417788	-8.835576	0.744532	*	*
PL.1.1	12	4	8.235466	8.235466	-8.470933	0.618783	*	*
PD.2	21	4	7.675851	7.675851	-7.351701	0.353455	*	*
KP.4.2.4	22	4	7.629331	7.629331	-7.258661	0.337902	*	*
KR.1.4	24	4	7.408788	7.408788	-6.817576	0.271173	*	*
KP.3.1.2	28	4	7.277693	7.277693	-6.555386	0.238115	*	*
JN.1.69	32	4	7.254637	7.254637	-6.509274	0.232236	*	*
JN.1.50.2	33	4	7.162322	7.162322	-6.324644	0.211189	*	*
LP.8.1.10	32	4	7.156197	7.156197	-6.312394	0.210136	*	*

|||||

LF.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7	58	6	305.993193	NaN	NaN	NaN	*	*	*
XFG.3	480	6	305.966793	295.966793	-249.933586	9.704455e-01	*	*
XFG.2	500	6	301.198751	283.660121	-225.320242	4.395189e-06		*
XFG.3.1	87	6	272.157898	262.157898	-182.315796	2.021372e-15		*
XFG.1	14	6	257.211449	247.211449	-152.422899	6.500454e-22		*
LF.7.1	165	16	219.915996	204.430262	-66.860524	1.713270e-40
LF.7.1.8	44	16	212.916100	197.408311	-52.816622	1.531364e-43
LF.7.7.1	188	12	206.168587	186.726282	-31.452563	3.504628e-48
LF.7.6	15	12	192.840632	182.234498	-22.468997	3.932419e-50
LF.7.1.2	26	16	191.151893	175.612183	-9.224366	5.217456e-53

Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 1349_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7390_C|A, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22286_C|A, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26149_T|C, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 58 (XFG): IGS-10285-CVDP-C599AD85-A1B5-4508-ABD3-28AF4ABD7F3A



Target: 530 samples        Number of changes: 150                                               
BC: LB.1.3.5 + XFG.3       BC BR: 5-6                    BC BR coord: 2792 - 2793        
Direction L1: <<           Initial region span: 1-5,7-150 Gap history (edge excluded): 5-7
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 1.12e-172 Rec. model vs L2: 1.44e-07                                           
Flags: Model_2BP_Bad_L1_opp

LB.1.3.5 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LB.1.3.5	275	5	12.164161	NaN	NaN	NaN	*	*	*
MC.19	221	5	9.972804	9.972804	-1.945608	1.119167e-01	*	*
LB.1.7	1971	6	8.001031	7.810114	2.379772	1.284244e-02	*	*
JN.2	574	4	7.993860	0.921611	16.156779	1.307250e-05	*	*
DM.1	33	3	7.229608	-5.145505	28.291011	3.036425e-08
BA.2.38.1	43	3	6.941385	-1.981407	21.962815	7.192909e-07
XBB.1.28	11	3	6.519127	-2.403665	22.807331	4.702506e-07
BQ.1.1.23	644	3	5.352364	-7.019638	32.039276	4.656508e-09
BA.5.1.30	4775	3	4.442524	-4.481106	26.962213	5.904299e-08
BA.4.6.5	1612	3	4.029062	-8.788269	35.576537	7.931569e-10

|||||

XFG.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	7	296.978611	NaN	NaN	NaN	*	*	*
LF.7	58	7	296.906879	286.906879	-235.813758	9.277435e-01	*	*
XFG.2	500	7	291.857845	281.857845	-225.715690	5.976023e-03	*	*
XFG.3.1	87	7	266.956245	256.956245	-175.912489	9.126582e-14		*
XFG.1	14	7	247.918714	237.918714	-137.837428	4.937564e-22		*
LF.7.1	165	16	211.677293	195.114352	-52.228703	1.269221e-40
LF.7.1.8	44	16	204.691375	188.106379	-38.212758	1.145864e-43
LF.7.7.1	188	12	197.858755	189.880014	-41.760027	6.760920e-43
LF.7.1.2	26	3	186.521031	180.808011	-23.616022	7.779557e-47
LF.7.6	15	12	184.476889	172.793547	-7.587094	2.570896e-50

Target sequence

, 241_C|T, 514_T|C, 670_T|G, 897_C|A, 2790_C|T, 2857_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7760_G|A, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10369_C|G, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12865_T|C, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23006_23008, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

 Case 63 (XEK): OZ255297



Target: 289 samples       Number of changes: 143                                                   
BC: XEK.1 + XEC.2         BC BR: 15-16                    BC BR coord: 5705 - 5706          
Direction L1: <<          Initial region span: 1-13,17-143 Gap history (edge excluded): 13-17
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 5.83e-01                                                            
Rec. model vs L1: 2.00e-15 Rec. model vs L2: 2.65e-32                                               
Flags: Model_1BP_Best

XEK.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEK.1	88	13	27.091884	NaN	NaN	NaN	*	*	*
XEK.1.2	33	13	27.008002	25.556273	-17.112547	9.277435e-01	*	*
XEK.1.1	11	13	18.923304	17.471575	-0.943150	2.858624e-04	*	*
XEK.7	12	10	16.741721	7.349839	19.300323	1.151057e-08
XEK.6	23	10	16.697269	7.392398	19.215203	1.198033e-08
XEK.2	67	10	16.597472	7.292601	19.414799	1.089458e-08
JN.1	17255	13	13.628505	-6.371495	46.742989	1.266417e-14		*
XEC.2.1	265	8	13.015012	-29.018407	92.036813	1.844194e-24
KP.3.1.1	12013	14	12.644192	2.644192	28.711616	1.041697e-10		*
KP.2.3	4440	10	12.483385	-15.374951	64.749902	1.555087e-18

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	17	198.006872	NaN	NaN	NaN	*	*	*
XEK.1	88	3	196.323932	160.699772	-39.399544	1.385445e-12
KP.3.3	1715	16	191.808188	191.808188	-101.616376	4.492525e+01	*	*
XEK.1.2	33	3	188.746271	153.194564	-24.389127	7.624460e-16
XEC.14	193	25	183.025282	156.750509	-31.501018	2.667632e-14
XEK.5	28	3	182.036925	164.678748	-47.357496	7.414489e-11
XEC.31	66	25	180.525047	154.250273	-26.500547	2.189726e-15
XEK.1.1	11	3	179.774906	152.307896	-22.615793	3.146723e-16
XEC.33	169	52	177.108571	145.738331	-9.476661	4.411068e-19
XEC.19	59	25	174.143674	147.868901	-13.737802	3.711855e-18

Target sequence

, 241_C|T, 583_C|T, 593_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3505_C|T, 3565_T|C, 3774_G|A, 4184_G|A, 4321_C|T, 4921_C|T, 5701_T|C, 5950_G|T, 6183_A|G, 7113_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9286_C|T, 9344_C|T, 9391_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16575_C|T, 17410_C|T, 18163_A|G, 18354_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19419_G|A, 19716_C|T, 19955_C|T, 20055_A|G, 21641_G|T, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25046_C|T, 25207_C|T, 25584_C|T, 25699_G|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 63 (XEK): USA/2025CV0302/2025



Target: 289 samples       Number of changes: 156                                                                          
BC: XEK.1 + FD.1.1 + XEK.1 BC BR: 140-141, 143-144                   BC BR coord: 27915 - 27916, 28270 - 28271      
Direction L1: >>          Initial region span: 1-140,142-143,144-156 Gap history (edge excluded): 140-144 -> 140-142
Alt. candidates: [], []                                                                                                          
Model 1BP/2BP comparison: 2BP vs 1BP: 1.14e-03                                                                                   
Rec. model vs L1: 1.08e-15 Rec. model vs L2: 0.00e+00                                                                      
Flags: Model_2BP_Best

XEK.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEK.1	88	140	218.708144	NaN	NaN	NaN	*	*	*
XEK.5	28	140	197.934589	198.147089	-60.294177	9.077973e-10		*
XEK.6	23	140	185.448321	185.314080	-34.628161	2.432152e-15		*
XEK.1.2	33	140	176.482309	176.653885	-17.307770	4.216970e-19		*
KP.2.3	4440	140	170.440721	172.920295	-9.840590	1.006724e-20		*
KP.3.3	1715	140	170.067375	182.555212	-29.110424	1.539352e-16		*
KP.3.1.1	12013	140	168.159935	175.356906	-14.713813	1.149258e-19		*
XEK.2	67	140	166.916784	167.171613	1.656774	3.204183e-23		*
JN.1	17255	140	157.012071	155.763339	24.473323	3.569347e-28		*
KP.3.1	1957	140	155.848681	160.692312	14.615375	4.914610e-26		*

|||||

FD.1.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
FD.1.1	218	142	14.812338	NaN	NaN	NaN	*	*	*
BA.5.1.26	94	142	12.465426	2.465426	1.069148	9.584720e-02	*	*
BA.1.9	133	142	9.574093	-0.425907	6.851814	5.326824e-03	*	*
JN.1.52	150	142	9.333521	-0.666479	7.332959	4.190229e-03	*	*
BA.5.1.9	242	142	8.376916	-1.623084	9.246168	1.604409e-03	*	*
CH.1.1.25	271	142	8.150554	-1.849446	9.698893	1.281146e-03	*	*
FY.8.1	29	143	7.147088	-12.852912	31.705824	2.129060e-08		*
LP.8.1.1	2345	142	6.607299	-3.392701	12.785403	2.732837e-04	*	*
XBB.1.5.72	569	143	6.485511	-13.514489	33.028978	1.100408e-08		*
XBB.1.15.1	11	143	6.037047	-13.962953	33.925906	7.016509e-09		*

|||||

XEK.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEK.1	88	144	0.25718	None	None	None	*	*	*

Target sequence

, 241_C|T, 593_C|T, 670_T|G, 829_C|T, 897_C|A, 1905_T|C, 2031_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3505_C|T, 3565_T|C, 4184_G|A, 4321_C|T, 5392_C|T, 5701_T|C, 6183_A|G, 7113_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9286_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10138_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16954_C|T, 17410_C|T, 17550_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21742_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G,
22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22994_A|G, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23287_T|C, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28039_T|C, 28131_.|T, 28132_C|T, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29200_C|T,
29510_A|C, 29734_29759, 29769_C|T

 Case 63 (XEK): USA/CA-CDPH-500147163/2025



Target: 289 samples         Number of changes: 155                                                               
BC: XEC.18 + KP.2.3 + XEC.18 BC BR: 4-5, 38-39                    BC BR coord: 896 - 897, 12788 - 12789    
Direction L1: <<            Initial region span: 1-4,21-38,39-155 Gap history (edge excluded): 4-39 -> 4-21
Alt. candidates: [], []                                                                                                 
Model 1BP/2BP comparison:   2BP vs 1BP: 5.76e-04                                                                        
Rec. model vs L1: 3.07e-45  Rec. model vs L2: 2.01e-60                                                           
Flags: Model_2BP_Best

XEC.18 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.18	165	4	5.612364	None	None	None	*	*	*

|||||

KP.2.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3	4440	21	22.489705	NaN	NaN	NaN	*	*	*
KP.2.3.9	23	21	17.600501	-58.325561	192.651121	4.398931e-16		*
LF.1.1	15	35	14.962994	-100.362404	276.724808	2.442185e-34
KP.2.5	66	35	14.159269	-83.013448	242.026896	8.329451e-27
JN.1	17255	22	13.638522	-1.820132	79.640265	1.524603e+09	*	*
JN.1.4	8971	22	12.484046	-2.778694	81.557388	5.837597e+08	*	*
KP.2.3.3	149	21	12.363388	-63.576142	203.152283	2.308347e-18		*
KP.3.1.1	12013	21	12.232672	-2.561748	81.123495	7.274094e+08	*	*
JN.1.38	247	35	12.157599	-76.653630	229.307260	4.816475e-24
JN.1.18.3	97	26	9.481472	-64.858185	205.716370	6.386055e-19

|||||

XEC.18 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.18	165	39	218.477804	NaN	NaN	NaN	*	*	*
XEC.2	921	21	215.781251	213.040631	-168.081261	1.588715e-05	*
XEC.2.3	28	39	213.459445	208.178265	-158.356529	1.231331e-07		*
XEC.8	592	39	213.200473	217.478622	-176.957244	1.346832e-03	*	*
XEC.2.1	265	58	206.298206	210.450130	-162.900260	1.191855e-06
XEC.33	169	39	202.522247	197.211178	-136.422356	2.119163e-12		*
KP.3.3	1715	21	200.745506	194.730451	-131.460901	1.774655e-13
XEC.40	52	39	197.970137	192.650121	-127.300241	2.217081e-14		*
XEC.36	30	39	197.663987	192.382806	-126.765612	1.700957e-14		*
XEK.1	88	21	196.758634	203.292911	-148.585821	9.307783e-10

Target sequence

, 241_C|T, 593_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3505_C|T, 3565_T|C, 3736_C|T, 3909_T|C, 4184_G|A, 4321_C|T, 4825_T|C, 5622_C|T, 5701_T|C, 5761_G|A, 6183_A|G, 6601_A|G,
7105_C|T, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9286_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 9808_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10969_C|T, 11042_G|T, 11288_11296, 11727_G|A,
12544_A|G, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19287_T|A, 19716_C|T, 19955_C|T, 20055_A|G,
21302_C|T, 21304_C|A, 21305_G|A, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994,
22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A,
22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28057_C|T, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29380_A|G,
29510_A|C

 Case 63 (XEK): USA/CA-LACPHL-AY11146/2025



Target: 289 samples        Number of changes: 148                                               
BC: XEK.1 + KP.2.6.2       BC BR: 145-146                    BC BR coord: 28958 - 28959  
Direction L1: >>           Initial region span: 1-145,146-148 Gap history (edge excluded):
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 5.28e-09 Rec. model vs L2: 4.25e-183                                          
Flags: Model_2BP_Bad_L1_opp

XEK.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEK.1	88	145	262.588514	NaN	NaN	NaN	*	*	*
XEK.5	28	145	249.494215	249.494215	-172.988430	2.055482e-06		*
XEK.6	23	145	247.789937	247.789937	-169.579875	3.736299e-07		*
XEK.2	67	145	242.190232	242.190232	-158.380463	1.381633e-09		*
XEK.1.2	33	145	239.778065	239.778065	-153.556130	1.240917e-10		*
XEK.1.1	11	145	230.983464	230.983464	-135.966929	1.879849e-14		*
KP.3.3	1715	148	223.631688	221.329767	-116.659534	1.205063e-18
XEC.2	921	148	210.420146	207.851622	-89.703244	1.685466e-24
XEK.7	12	145	206.481676	206.481676	-86.963353	4.282887e-25		*
KP.2.3	4440	148	200.201152	196.479239	-66.958479	1.944428e-29

|||||

KP.2.6.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.6.2	26	146	7.729416	NaN	NaN	NaN	*	*	*
GR.1	120	146	7.614753	7.614753	-9.229507	0.891366	*	*
HP.1.1	48	146	7.441734	7.441734	-8.883468	0.748264	*	*
XBB.1.5.62	311	146	7.154875	7.154875	-8.309750	0.562705	*	*
BF.12	89	146	7.111513	7.111513	-8.223025	0.537944	*	*
MC.17.1	10	146	6.813126	6.813126	-7.626251	0.400517	*	*
XBB.1.44	23	146	5.967853	5.967853	-5.935706	0.172045	*	*
XBB.1.17.1	134	146	5.825441	5.825441	-5.650883	0.148823	*	*
ED.2	223	146	5.694784	5.694784	-5.389568	0.130680	*	*
HU.1.1	72	146	5.556207	5.556207	-5.112413	0.113608	*	*

Target sequence

, 241_C|T, 593_C|T, 670_T|G, 897_C|A, 2338_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3505_C|T, 3565_T|C, 4184_G|A, 4321_C|T, 5701_T|C, 6183_A|G, 6636_C|T, 7113_C|T, 7119_C|T, 7842_A|G, 7843_C|T,
8293_C|T, 8393_G|A, 9286_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C,
14408_C|T, 14730_G|A, 15714_C|T, 15756_T|A, 16662_G|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21739_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T,
25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29095_C|T, 29510_A|C, 29734_29759

 Case 63 (XEK): USA/IL-CDC-LC1134516/2025



Target: 289 samples        Number of changes: 152                                                   
BC: XEK.6 + XEC.2          BC BR: 17-18                    BC BR coord: 6183 - 6184          
Direction L1: <<           Initial region span: 1-14,19-152 Gap history (edge excluded): 14-19
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 2.42e-29 Rec. model vs L2: 2.46e-29                                               
Flags: Model_2BP_Bad_L1_opp

XEK.6 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEK.6	23	14	17.392398	NaN	NaN	NaN	*	*	*
XEK.7	12	14	17.349839	0.959630	40.080740	9.607894e-01	*	*
XEK.2	67	14	17.292601	0.902392	40.195217	9.048374e-01	*	*
XEK.1	88	10	16.730292	-7.190950	56.381899	2.774139e-04	*
XEK.1.2	33	10	16.646411	-7.263402	56.526805	2.573689e-04	*
KP.3.1	1957	13	16.423531	-9.968212	61.936424	1.721034e-05	*	*
JN.1	17255	13	13.697315	-0.159116	42.318232	3.134862e-01	*	*
XEK.5	28	14	9.232507	-7.157702	56.315405	2.858624e-04	*	*
XEK.1.1	11	10	8.561713	-15.348101	72.696201	7.930220e-08
BA.5.2.18	582	4	5.301905	-84.479317	210.958634	7.525020e-38

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	19	249.213712	NaN	NaN	NaN	*	*	*
XEC.18	165	21	247.097740	217.097740	-138.195480	2.486437e-10
XEC.2.3	28	33	233.902806	190.959735	-85.919470	1.104383e-21
XEC.8	592	33	233.600505	218.908493	-141.816985	1.519325e-09
XEK.1	88	20	229.281364	209.281364	-122.562728	9.986072e-14		*
XEK.5	28	20	228.934746	208.934746	-121.869492	7.072339e-14		*
XEK.1.2	33	20	227.770867	199.342314	-102.684629	4.814016e-18		*
XEC.11.1	166	21	223.020012	183.873438	-71.746875	9.250035e-25
XEC.33	169	33	223.000437	192.002090	-88.004180	3.124540e-21
KP.3.3	1715	20	222.303587	214.525076	-133.050152	1.893517e-11		*

Target sequence

, 241_C|T, 248_G|T, 593_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3505_C|T, 3565_T|C, 3736_C|T, 4184_G|A, 4321_C|T, 5701_T|C, 5761_G|A, 5920_T|C, 6183_A|G, 6601_A|G, 6781_C|T,
7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9286_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10969_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T,
12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19287_T|A, 19716_C|T, 19955_C|T, 20055_A|G, 20262_A|G, 21302_C|T, 21304_C|A,
21305_G|A, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A,
22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 63 (XEK): USA/NY-PRL-250415_83G08/2025



Target: 289 samples          Number of changes: 149                                                          
BC: XEK.6 + KP.3.3.10 + XEK.6 BC BR: 3-4, 8-9                   BC BR coord: 672 - 673, 3430 - 3431    
Direction L1: <<             Initial region span: 1-3,5-8,9-149 Gap history (edge excluded): 3-9 -> 3-5
Alt. candidates: [], []                                                                                             
Model 1BP/2BP comparison:    2BP vs 1BP: 7.89e-08                                                                   
Rec. model vs L1: 8.01e-08   Rec. model vs L2: 9.53e-79                                                      
Flags: Model_2BP_Best

XEK.6 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEK.6	23	3	7.058661	None	None	None	*	*	*

|||||

KP.3.3.10 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.3.10	55	5	11.104350	NaN	NaN	NaN	*	*	*
B.1.493	13	7	7.591531	-25.885472	73.770943	1.898418e-12
JG.2	72	6	5.844423	-25.374283	72.748565	3.161419e-12		*
CP.5	75	6	5.817588	-17.193333	56.386666	1.128265e-08		*
AY.104	28	7	5.725663	-30.003001	82.006002	3.083889e-14
JN.1	17255	4	5.427866	5.427866	11.144269	7.556551e+01	*	*
N.5	93	7	5.218415	-24.781585	71.563169	5.731751e-12
EG.2	163	6	5.035172	-14.964828	51.929657	1.049271e-07		*
JN.1.4	8971	5	4.643715	-1.330014	24.660027	8.759775e-02	*	*
AY.43.2	141	8	4.105222	-25.941812	73.883625	1.796825e-12

|||||

XEK.6 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEK.6	23	9	237.473449	NaN	NaN	NaN	*	*	*
XEK.1	88	15	235.494901	241.448869	-168.897738	4.595926e-02	*
XEK.5	28	9	234.567373	241.670486	-169.340971	5.726876e-02	*	*
XEC.9	305	22	220.499829	187.240374	-60.480747	1.316040e-25
XEK.2	67	9	219.210596	226.313709	-138.627417	1.228361e-08		*
XEK.1.2	33	15	214.099349	219.969435	-125.938871	2.156391e-11
KP.3.3	1715	16	213.351318	203.284283	-92.568566	1.223275e-18
XEK.1.1	11	15	213.350667	219.220754	-124.441508	1.018607e-11
XEC.2	921	16	209.533185	181.313082	-48.626163	3.516206e-28
XEC.29	135	22	208.604975	157.710619	-1.421239	1.970394e-38

Target sequence

, 241_C|T, 593_C|T, 670_T|G, 829_C|T, 897_C|A, 2790_C|T, 3037_C|T, 3048_A|G, 3431_G|T, 3505_C|T, 3565_T|C, 4184_G|A, 4321_C|T, 5392_C|T, 5701_T|C, 6183_A|G, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9286_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16954_C|T, 17285_C|T, 17410_C|T, 18163_A|G, 18171_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19080_A|G, 19716_C|T, 19955_C|T, 20055_A|G, 21077_C|T, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21742_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T,
25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27481_C|T, 27807_C|T,
27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 63 (XEK): IGS-10285-CVDP-5E07523F-5968-4EAF-99D3-0FF692B7D24D



Target: 289 samples          Number of changes: 144                                                        
BC: XEK.5 + B.1.1.434 + XEK.5 BC BR: 5-6, 8-9                   BC BR coord: 2792 - 2793, 3430 - 3431
Direction L1: <<             Initial region span: 1-5,6-8,9-144 Gap history (edge excluded): 5-9 ->  
Alt. candidates: [], []                                                                                           
Model 1BP/2BP comparison:    2BP vs 1BP: 1.85e-08                                                                 
Rec. model vs L1: 1.47e-14   Rec. model vs L2: 0.00e+00                                                    
Flags: Model_2BP_Best

XEK.5 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEK.5	28	5	3.603332	None	None	None	*	*	*

|||||

B.1.1.434 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
B.1.1.434	1274	6	8.009487	NaN	NaN	NaN	*	*	*
XBB.2.3.14	18	7	6.536776	-3.463224	12.926449	0.000010	*	*
B.1.1.304	143	7	6.536776	-3.463224	12.926449	0.000010	*	*
AZ.5	21	7	6.536776	-3.463224	12.926449	0.000010	*	*
KP.3.1.5	45	7	6.536776	-3.463224	12.926449	0.000010	*	*
NL.11	57	7	6.131310	-3.868690	13.737379	0.000007		*
KP.3.1	1957	6	5.331302	5.331302	-4.662603	0.068563	*	*
B.1.1.306	97	8	4.523128	-5.493820	16.987640	0.000001
JE.1.1.1	46	7	4.499894	-5.500106	17.000213	0.000001		*
XBB.1.5.77	308	6	4.394709	4.394709	-2.789418	0.026917	*	*

|||||

XEK.5 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEK.5	28	9	287.216513	NaN	NaN	NaN	*	*	*
XEK.1	88	15	280.497542	291.156073	-274.312145	1.397940e+00	*
XEK.6	23	9	276.969235	288.732459	-269.464917	1.236871e-01	*	*
XEK.2	67	1	275.976074	283.643991	-259.287982	7.654857e-04	*
XEK.1.2	33	15	270.672104	281.246753	-254.493507	6.944330e-05	*
XEK.1.1	11	15	266.017825	276.497165	-244.994329	6.008022e-07
XEC.2	921	16	262.221896	238.686638	-169.373276	2.280642e-23
KP.3.3	1715	16	260.095641	254.704244	-201.408487	2.067544e-16
XEC.2.1	265	27	257.006081	223.302575	-138.605150	4.770985e-30
XEC.8	592	16	254.346062	250.548209	-193.096417	3.243107e-18

Target sequence

, 241_C|T, 593_C|T, 670_T|G, 897_C|A, 2790_C|T, 2947_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3505_C|T, 3565_T|C, 4184_G|A, 4321_C|T, 4780_C|T, 5701_T|C, 6183_A|G, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9286_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
14556_T|C, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23621_G|A, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 71 (XFB): Denmark/DCGC-692189/2025



Target: 9 samples         Number of changes: 148                                                   
BC: KP.2.3 + XFB.3        BC BR: 15-16                    BC BR coord: 7118 - 7119          
Direction L1: <<          Initial region span: 1-15,17-148 Gap history (edge excluded): 15-17
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 1.21e-01                                                            
Rec. model vs L1: 2.16e-54 Rec. model vs L2: 1.73e-13                                               
Flags: Model_1BP_Best

KP.2.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3	4440	15	27.676390	NaN	NaN	NaN	*	*	*
MF.1	35	12	27.284261	-11.627622	67.255245	8.512466e-18
KP.3.1.1	12013	15	26.134250	26.134250	-8.268500	2.143811e-01	*	*
MC.9	298	12	25.342468	23.335709	-2.671418	1.303653e-02	*
LF.7.9.3	20	10	20.996396	-10.469164	64.938327	2.715420e-17
XFB.3	56	10	20.989870	3.921235	36.157530	4.823192e-11
BA.2.86.1	1343	14	20.007899	10.007899	23.984202	2.129060e-08		*
JN.1.7.6	67	10	19.957551	-14.302615	72.605230	5.865670e-19
JN.1.65.1	46	10	19.947679	-27.922911	99.845822	7.132254e-25
KP.2.8	51	10	19.758085	-0.893584	45.787167	3.910269e-13

|||||

XFB.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFB.3	56	17	246.995466	NaN	NaN	NaN	*	*	*
KP.3.1.1	12013	1	233.622447	207.488197	-126.976394	1.535116e-13
MC.1	932	1	222.716027	209.045941	-130.091882	7.268909e-13
MC.24	831	14	212.260699	204.266507	-120.533013	6.102975e-15
MC.19	221	17	197.642832	187.642832	-87.285664	3.694599e-22		*
MC.28	304	1	196.599073	181.315025	-74.630050	6.583900e-25
KP.3.1	1957	1	191.675662	177.025984	-66.051968	9.023186e-27
MC.21.1	187	17	188.103654	178.103654	-68.207308	2.657039e-26		*
MC.10.1	650	17	180.678112	170.678112	-53.356224	1.584023e-29		*
MC.42	84	1	180.300534	164.720658	-41.441316	4.086639e-32

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4218_G|A, 4321_C|T, 6040_C|T, 6183_A|G, 7113_C|T, 7471_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12616_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13121_A|T, 13339_T|C, 14408_C|T,
15372_G|T, 15714_C|T, 15756_T|A, 17334_G|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19722_A|G, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21633_21641,
21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22111_G|T, 22131_G|C, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22858_C|T, 22865_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A,
23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24022_T|C, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T,
25584_C|T, 25595_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26690_G|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27752_C|T,
27807_C|T, 27810_T|C, 28211_A|G, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 71 (XFB): OZ285853



Target: 9 samples                 Number of changes: 151                                                                          
BC: KP.3.1.1 + LF.7.1.8 + KP.3.1.1 BC BR: 138-139, 141-142                   BC BR coord: 27387 - 27388, 27810 - 27811      
Direction L1: >>                  Initial region span: 1-138,139-141,144-151 Gap history (edge excluded): 138-144 -> 141-144
Alt. candidates: [], []                                                                                                                  
Model 1BP/2BP comparison:         2BP vs 1BP: 4.23e-01                                                                                   
Rec. model vs L1: 1.26e-07        Rec. model vs L2: 1.67e-189                                                                     
Flags: Model_2BP_Best

KP.3.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.1	12013	138	234.570858	NaN	NaN	NaN	*	*	*
MC.1	932	138	208.439599	206.724207	-95.448413	1.500834e-12		*
XFB.3	56	150	207.845939	213.242383	-108.484765	1.013354e-09
KP.3.1	1957	138	194.065974	181.491795	-44.983591	1.647826e-23		*
MC.24	831	138	192.056902	179.435778	-40.871556	2.110748e-24		*
MC.13	807	138	185.570478	172.981527	-27.963053	3.319445e-27		*
MC.10	221	138	183.579011	171.028903	-24.057806	4.722709e-28		*
MC.19	221	138	181.928622	169.357382	-20.714764	8.846020e-29		*
KP.2.3	4440	138	180.476340	179.277858	-40.555715	1.807676e-24		*
MC.10.1	650	138	179.499675	167.005837	-16.011673	8.436376e-30		*

|||||

LF.7.1.8 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7.1.8	44	141	10.292769	NaN	NaN	NaN	*	*	*
XEC.3	29	141	10.039505	10.039505	-10.079011	7.749165e-01	*	*
XBF.7.1	13	140	9.792451	-0.207549	10.415099	2.739911e-05	*	*
XFG.2	500	141	9.590088	9.590088	-9.180177	4.941086e-01	*	*
MC.23	64	141	9.247918	9.247918	-8.495836	3.516918e-01	*	*
JN.1.29	69	141	9.172695	9.172695	-8.345390	3.262798e-01	*	*
KP.3.3.3	288	141	7.743841	7.743841	-5.487682	7.808167e-02	*	*
AY.34.2	258	139	6.420271	-15.653220	41.306439	5.371038e-12
KP.2.2	1334	141	6.210864	6.210864	-2.421728	1.682314e-02	*	*
BA.2.75.4	36	140	6.208932	-3.791068	17.582136	7.637693e-07		*

|||||

KP.3.1.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.1	12013	144	7.419819	None	None	None	*	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1758_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5672_C|T, 6183_A|G, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 8809_C|T, 9344_C|T, 9424_A|G,
9534_C|T, 9565_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12043_C|T, 12235_A|C, 12616_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13121_A|T, 13339_T|C,
14408_C|T, 15372_G|T, 15714_C|T, 15756_T|A, 17334_G|T, 17410_C|T, 18163_A|G, 18449_G|T, 18492_A|G, 18894_C|T, 19722_A|G, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21633_21641, 21653_21655, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22111_G|T, 22131_G|C, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22666_A|G, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22858_C|T, 22865_G|T,
22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25595_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27546_T|C, 27807_C|T, 27810_T|C, 27982_C|T, 28211_A|G, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C

 Case 72 (XEC): BHR/25000004638/2025



Target: 5350 samples      Number of changes: 146                                                   
BC: XEC.8 + XEC.2         BC BR: 13-14                    BC BR coord: 6183 - 6184          
Direction L1: <<          Initial region span: 1-13,17-146 Gap history (edge excluded): 13-17
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 1.12e-02                                                            
Rec. model vs L1: 1.13e-21 Rec. model vs L2: 5.71e-18                                               
Flags: Model_1BP_Best

XEC.8 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.8	592	13	27.259665	NaN	NaN	NaN	*	*	*
XEC.4.1	68	13	16.558685	16.558685	-7.117369	2.254494e-05	*	*
XEC.5	126	13	15.907539	15.907539	-5.815079	1.176949e-05	*	*
XEC.39	155	13	15.705718	15.705718	-5.411435	9.587983e-06		*
XEC.32	42	15	14.250469	5.079158	15.841683	2.329960e-10
MC.10.1	650	14	14.198579	8.716119	8.567761	8.830979e-09		*
KP.3.1.1	12013	13	13.612549	13.612549	-1.225098	1.185910e-06		*
LY.1	178	13	11.356933	11.356933	3.286133	1.237503e-07		*
MC.24	831	13	9.510400	9.510400	6.979199	1.955568e-08		*
KP.3.3	1715	13	8.726622	8.726622	8.546756	8.919731e-09		*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	17	232.121365	NaN	NaN	NaN	*	*	*
XEK.5	28	17	231.627599	197.240788	-106.481577	7.597014e-03	*	*
XEC.29	135	17	224.351842	185.788764	-83.577528	8.090421e-08		*
XEC.32	42	7	219.374555	205.300617	-122.601234	2.404675e+01	*
XEC.18	165	17	216.686713	186.686713	-85.373427	1.979998e-07		*
XEC.39	155	17	215.163625	185.163625	-82.327250	4.330490e-08		*
XEC.30	135	17	213.027734	197.021805	-106.043609	6.096747e-03	*	*
XEC.2.2	273	17	212.493655	182.493655	-76.987309	2.998961e-09		*
XEC.31	66	17	211.301202	181.301202	-74.602404	9.077973e-10		*
XEC.3	29	17	211.142481	181.142481	-74.284963	7.735738e-10		*

Target sequence

, 241_C|T, 670_T|G, 745_C|T, 897_C|A, 2060_G|A, 2659_G|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6362_G|A, 7318_C|T, 7360_G|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15162_A|G, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18186_G|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22893_A|C, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28851_G|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759, 29762_C|T

 Case 72 (XEC): BHR/25020232316/2025



Target: 5350 samples      Number of changes: 149                                                               
BC: XEC.2 + XEC.25 + XEC.2 BC BR: 4-5, 13-14                   BC BR coord: 1884 - 1885, 6183 - 6184     
Direction L1: <<          Initial region span: 1-4,5-13,15-149 Gap history (edge excluded): 4-15 -> 13-15
Alt. candidates: [], []                                                                                               
Model 1BP/2BP comparison: 2BP vs 1BP: 2.64e-04                                                                        
Rec. model vs L1: 9.75e-26 Rec. model vs L2: 4.14e-39                                                           
Flags: Model_2BP_Best

XEC.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	4	4.959443	None	None	None	*	*	*

|||||

XEC.25 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.25	13	13	28.661750	NaN	NaN	NaN	*	*	*
XEC.8.1	12	14	15.688113	10.273328	3.453344	1.036325e-08		*
XEC.24.1	18	9	14.603690	10.303181	3.393638	1.067886e-08
XEC.19	59	9	14.603690	3.572575	16.854850	1.275625e-11
XEC.34	22	9	14.603690	10.360339	3.279322	1.128265e-08
XEC.11.1	166	9	14.603690	1.156036	21.687927	1.134306e-12
XEC.17	13	9	14.603690	10.360339	3.279322	1.128265e-08
XEC.32	42	9	14.603690	10.360339	3.279322	1.128265e-08
XEC.4.6.1	13	9	14.603690	10.360339	3.279322	1.128265e-08
XEC.4.1.4	23	9	14.603690	5.289815	13.420370	7.088233e-11

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	15	209.885495	NaN	NaN	NaN	*	*	*
XEC.39	155	32	202.892756	171.031197	-32.062394	2.062206e-15
KP.3.3	1715	42	202.230148	189.193822	-68.387644	1.596950e-07
XEC.2.1	265	42	199.430248	164.960131	-19.920261	4.766116e-18
XEC.4	192	42	192.163249	157.406879	-4.813757	2.494996e-21
XEC.29	135	42	185.229244	165.987965	-21.975931	1.335020e-17
KP.3.1.1	12013	47	180.607989	177.888882	-45.777763	1.966040e-12
XEC.18	165	42	179.195020	154.932544	0.134911	2.110388e-22
XEC.31	66	42	173.452251	138.686316	32.627369	1.849597e-29
XEC.40	52	42	173.440951	132.341371	45.317258	3.246972e-32

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1884_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3971_G|A, 4184_G|A, 4321_C|T, 6183_A|G, 7420_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10733_C|T, 11042_G|T, 11074_C|T, 11288_11296, 11727_G|A, 12043_C|T, 12781_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15105_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18151_T|C, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 19964_T|C, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G,
22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A,
23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
25629_T|C, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28453_C|T, 28674_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29733_29758, 29759_G|T

 Case 72 (XEC): BHR/25040003778/2025



Target: 5350 samples       Number of changes: 144                                               
BC: NM.1 + XEC.13          BC BR: 4-5                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-4,7-144 Gap history (edge excluded): 4-7
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 1.03e-212 Rec. model vs L2: 6.04e-09                                           
Flags: Model_2BP_Bad_L1_opp

NM.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
NM.1	41	4	10.513390	NaN	NaN	NaN	*	*	*
JN.1.1.7	17	4	8.449310	8.449310	-8.898619	0.126818	*	*
MK.2	15	4	7.881326	7.881326	-7.762651	0.071719	*	*
MC.9.1	15	4	7.881326	7.881326	-7.762651	0.071719	*	*
PA.1.4	14	4	7.876211	7.876211	-7.752421	0.071361	*	*
JN.2.2	16	4	7.816787	7.816787	-7.633574	0.067206	*	*
MC.5	19	4	7.644937	7.644937	-7.289874	0.056699	*	*
JN.1.56	21	4	7.496063	7.496063	-6.992126	0.048801	*	*
LF.7.1.3	24	4	7.368762	7.368762	-6.737525	0.043067	*	*
KP.4.2	75	4	7.302649	7.302649	-6.605299	0.040357	*	*

|||||

XEC.13 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.13	30	7	265.469966	NaN	NaN	NaN	*	*	*
XEC.2	921	14	261.124216	233.725098	-169.450196	6.710049e-13
XEC.16	23	7	256.091262	252.377663	-206.755326	8.481824e-05	*	*
XEC.31	66	14	245.788644	234.600906	-171.201813	1.609657e-12
MC.24.1	25	7	245.783893	241.416368	-184.832735	1.467068e-09		*
XEC.39	155	7	237.583806	233.863734	-169.727469	7.718393e-13		*
KP.3.3	1715	15	236.907737	228.296675	-158.593350	2.941079e-15
XEC.9	305	15	235.877310	230.107992	-162.215984	1.806139e-14
XEC.14	193	3	232.297944	228.083666	-158.167331	2.383992e-15
XEC.28	39	14	231.637429	221.387462	-144.774924	2.934484e-18

Target sequence

, 241_C|T, 670_T|G, 835_C|T, 897_C|A, 2060_G|A, 2286_G|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5184_C|A, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13821_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 15849_T|C,
17410_C|T, 18163_A|G, 18315_G|A, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21595_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27101_T|C, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): Denmark/DCGC-692047/2025



Target: 5350 samples      Number of changes: 145                                                 
BC: XEC.25 + XEC.2        BC BR: 9-10                    BC BR coord: 3566 - 3567         
Direction L1: <<          Initial region span: 1-9,16-145 Gap history (edge excluded): 9-16
Alt. candidates: [], []                                                                                 
Model 1BP/2BP comparison: 1BP vs 2BP: 3.55e-01                                                          
Rec. model vs L1: 3.54e-25 Rec. model vs L2: 4.61e-17                                             
Flags: Model_1BP_Best

XEC.25 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.25	13	9	24.715389	NaN	NaN	NaN	*	*	*
XEC.4	192	9	20.865923	20.865923	-21.731845	2.127974e-02	*	*
XEC.9	305	9	20.381513	20.381513	-20.763027	1.310187e-02	*	*
XEC.8	592	9	20.371099	20.371099	-20.742198	1.297151e-02	*	*
KP.3.3	1715	12	15.994590	14.104611	-8.209223	2.466809e-05	*
KP.3.1	1957	12	15.459081	12.316639	-4.633278	4.118589e-06
MC.24	831	12	15.277126	13.356415	-6.712830	1.165238e-05	*
XEC.39	155	12	13.565774	9.270302	1.459396	1.960296e-07
KP.3.1.12	39	4	11.473441	0.462399	19.075202	2.925414e-11
KP.3.1.1	12013	12	11.384515	9.735863	0.528274	3.120820e-07

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	16	253.679803	NaN	NaN	NaN	*	*	*
XEC.9	305	1	225.983668	205.602154	-113.204308	1.761245e-12
KP.3.3	1715	16	225.823976	206.945150	-115.890299	6.759988e-12		*
XEK.5	28	31	222.445529	182.314188	-66.628377	1.359167e-22
XEC.32	42	16	220.030730	195.787379	-93.574758	9.620984e-17		*
XEC.38	34	16	219.996578	195.753227	-93.506455	9.336641e-17		*
XEC.33	169	31	219.238350	190.658688	-83.317375	5.720846e-19
XEC.16	23	16	218.994518	194.751167	-91.502335	3.417627e-17		*
XEC.39	155	5	218.684899	204.120471	-110.240942	4.009258e-13
XEK.1	88	16	217.360017	171.978279	-45.956558	4.414072e-27		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1102_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3768_C|T, 4184_G|A, 4321_C|T, 5518_G|A, 6183_A|G, 6317_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11962_C|T, 12781_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14055_G|T, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25665_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29167_C|T, 29510_A|C, 29734_29759, 29769_C|T

 Case 72 (XEC): Denmark/DCGC-692052/2025



Target: 5350 samples      Number of changes: 143                                                               
BC: XEC.24 + JN.1 + XEC.24 BC BR: 4-5, 15-16                   BC BR coord: 2060 - 2061, 5620 - 5621     
Direction L1: <<          Initial region span: 1-4,5-13,16-143 Gap history (edge excluded): 4-16 -> 13-16
Alt. candidates: [], []                                                                                               
Model 1BP/2BP comparison: 2BP vs 1BP: 2.81e-17                                                                        
Rec. model vs L1: 8.65e-26 Rec. model vs L2: 1.59e-48                                                           
Flags: Model_2BP_Best

XEC.24 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.24	11	4	11.00522	None	None	None	*	*	*

|||||

JN.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1	17255	13	15.465153	NaN	NaN	NaN	*	*	*
LF.7.1.2	26	5	7.175400	-28.584526	95.169053	6.197319e-19
KP.3.1.1	12013	9	7.019484	0.224152	37.551696	2.014781e-06
BA.5.2.6	3344	5	5.409616	-32.560673	103.121345	1.163813e-20
DF.1	256	5	4.888319	-48.472106	134.944212	1.433039e-27
BQ.1.1.8	1026	5	4.598685	-50.153869	138.307737	2.657491e-28
BA.5.1.23	4202	8	4.448381	-18.040685	74.081369	2.354177e-14
XFG.3	480	5	4.259710	-39.431978	116.863956	1.208593e-23
AY.47	22935	5	4.030663	-68.675780	175.351559	2.406235e-36
B.1.577	618	5	4.007008	-74.434966	186.869931	7.582315e-39

|||||

XEC.24 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.24	11	16	256.811319	NaN	NaN	NaN	*	*	*
XEC.18	165	16	250.257031	261.244014	-246.488029	1.401797e-03	*	*
XEC.6	45	16	249.390178	260.372925	-244.745850	5.872852e-04	*	*
XEC.17	13	16	247.601456	258.606676	-241.213352	1.000340e-04	*	*
XEC.31	66	16	244.931072	255.905758	-235.811516	6.722839e-06		*
XEC.28	39	16	244.226999	255.153600	-234.307200	3.175644e-06		*
XEC.14	193	16	244.192137	255.171219	-234.342438	3.223638e-06		*
XEC.2	921	16	244.140724	238.822282	-201.644565	2.556416e-13		*
XEC.19	59	16	243.976078	254.929112	-233.858224	2.535804e-06		*
XEC.36	30	16	242.546123	253.551344	-231.102687	6.379538e-07		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2139_A|G, 2589_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3506_A|G, 3565_T|C, 4184_G|A, 4321_C|T, 4891_C|T, 5619_T|C, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 14790_C|A, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24760_T|C, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28744_C|T,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): Denmark/DCGC-692055/2025



Target: 5350 samples      Number of changes: 147                                                               
BC: XEC.2 + XEC.25 + XEC.2 BC BR: 5-6, 11-12                   BC BR coord: 896 - 897, 3566 - 3567       
Direction L1: <<          Initial region span: 1-5,6-11,18-147 Gap history (edge excluded): 5-18 -> 11-18
Alt. candidates: [], []                                                                                               
Model 1BP/2BP comparison: 2BP vs 1BP: 5.25e-01                                                                        
Rec. model vs L1: 4.80e-17 Rec. model vs L2: 5.43e-26                                                           
Flags: Model_2BP_Best

XEC.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	5	8.393377	None	None	None	*	*	*

|||||

XEC.25 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.25	13	11	19.996570	NaN	NaN	NaN	*	*	*
XEC.4	192	11	16.162852	16.162852	-18.325703	2.170962e-02	*	*
XEC.8	592	11	15.721092	15.721092	-17.442183	1.391205e-02	*	*
XEC.9	305	11	15.699037	15.699037	-17.398074	1.363657e-02	*	*
KP.3.3	1715	14	11.314662	9.424684	-4.849367	2.567482e-05	*
KP.3.1	1957	14	10.777917	7.635475	-1.270950	4.286672e-06
MC.24	831	14	10.584958	8.664247	-3.328494	1.200725e-05	*
XEC.39	155	14	8.859900	4.564428	4.871144	1.989922e-07
JD.1.1.5	61	6	6.859216	-22.059689	58.119379	5.441837e-19
KP.3.1.12	39	6	6.806573	-4.204469	22.408939	3.090819e-11

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	18	253.050390	NaN	NaN	NaN	*	*	*
XEC.9	305	1	229.442273	213.743236	-119.486472	2.575442e-12
KP.3.3	1715	18	225.081448	215.514144	-123.028288	1.512004e-11		*
XEK.5	28	33	221.657914	191.452515	-74.905030	5.375610e-22
XEC.38	34	18	219.454357	204.687530	-101.375061	3.008259e-16		*
XEC.32	42	18	219.370547	201.831408	-95.662816	1.722793e-17		*
XEC.33	169	33	218.603237	198.156206	-88.312412	4.367177e-19
XEC.16	23	18	218.223071	200.971993	-93.943986	7.290205e-18		*
XEC.39	155	7	218.013879	211.429158	-114.858316	2.543666e-13
XEC.36	30	16	216.813606	207.841698	-107.683396	7.020093e-15

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1102_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3768_C|T, 4184_G|A, 4321_C|T, 5518_G|A, 6183_A|G, 6317_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11962_C|T, 12781_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C,
14055_G|T, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G,
22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25665_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29167_C|T, 29510_A|C, 29734_29759, 29769_C|T

 Case 72 (XEC): Denmark/DCGC-692133/2025



Target: 5350 samples       Number of changes: 149                                                 
BC: LB.1.4.1 + XEC.2       BC BR: 15-16                   BC BR coord: 4387 - 4388         
Direction L1: <<           Initial region span: 1-5,16-149 Gap history (edge excluded): 5-16
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  -                                                                             
Rec. model vs L1: 2.29e-145 Rec. model vs L2: 2.36e-07                                             
Flags: Model_2BP_Bad_L1_opp

LB.1.4.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LB.1.4.1	74	5	9.746843	NaN	NaN	NaN	*	*	*
JN.1.9	576	5	8.679148	-20.870652	93.741304	5.364643e+02	*	*
MC.6	366	5	8.271496	-28.499733	108.999467	2.605397e-01	*	*
BA.5.2.48	267	4	7.771518	-68.166895	188.333789	1.547331e-18		*
JN.1.43	317	5	7.698286	-21.859784	95.719568	1.993376e+02	*	*
BA.5.2.16	361	4	5.420985	-64.364757	180.729515	6.916754e-17		*
XBB.1.21	24	3	5.414703	-72.054615	196.109231	3.163572e-20
DV.1.1	254	4	4.961095	-85.316881	222.633761	5.513571e-26		*
NM.2	28	5	4.868087	-24.667766	101.335532	1.200112e+01	*	*
BF.31	90	4	4.838919	-64.932750	181.865499	3.911600e-17		*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	16	243.378221	NaN	NaN	NaN	*	*	*
XEC.4	192	17	214.047209	204.047209	-122.094419	8.260885e-18		*
XEC.33	169	17	212.307018	202.307018	-118.614035	1.449954e-18		*
XEC.31	66	17	208.782562	198.782562	-111.565125	4.291781e-20		*
XEC.28	39	17	208.499160	191.524620	-97.049239	3.017586e-23		*
XEC.8	592	14	200.890310	198.745143	-111.490286	4.123498e-20
XEC.2.2	273	16	200.522431	200.522431	-115.044861	2.432980e-19		*
XEC.18	165	17	200.196005	190.196005	-94.392009	7.980829e-24		*
XEC.2.1	265	17	198.341674	188.341674	-90.683347	1.248624e-24		*
XEC.17	13	17	197.601456	187.601456	-89.202911	5.957359e-25		*

Target sequence

, 44_C|T, 180_C|T, 241_C|T, 670_T|G, 897_C|A, 1729_G|T, 2060_G|A, 2374_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4067_G|A, 4184_G|A, 4321_C|T, 4890_C|T, 6183_A|G, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11681_C|T, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13452_C|T,
13458_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 16474_A|G, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19779_A|G, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T,
25493_C|T, 25584_C|T, 25983_A|G, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27370_C|T, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): Denmark/DCGC-692246/2025



Target: 5350 samples      Number of changes: 145                                             
BC: KP.3.1.1 + XEC.2      BC BR: 16-17                    BC BR coord: 6660 - 6661    
Direction L1: <<          Initial region span: 1-16,17-145 Gap history (edge excluded):
Alt. candidates: [], []                                                                             
Model 1BP/2BP comparison: 1BP vs 2BP: 3.41e-03                                                      
Rec. model vs L1: 5.14e-63 Rec. model vs L2: 2.55e-24                                         
Flags: Model_1BP_Best

KP.3.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.1	12013	16	20.410738	NaN	NaN	NaN	*	*	*
XEC.35.1	28	13	17.890032	1.499823	39.000354	6.130436e-09
XEC.23	142	13	17.704623	-3.773639	49.547277	3.137530e-11
XEC.4.7	13	13	17.629701	-7.748836	57.497673	5.892063e-13
XEC.17	13	13	16.675670	0.285461	41.429078	1.818962e-09
XEC.15	127	13	16.658880	12.792759	16.414482	4.930007e-04	*
XEC.4	192	13	16.214163	-0.176046	42.352092	1.148281e-09
XEC.38	34	13	16.166447	-0.223762	42.447523	1.092278e-09
XEC.5	126	13	16.154980	-0.235229	42.470458	1.081410e-09
XEC.29	135	13	16.145763	-14.241346	70.482691	8.947387e-16

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	17	240.728994	NaN	NaN	NaN	*	*	*
XEC.18	165	17	235.479842	235.479842	-194.959684	5.247518e-03	*	*
XEC.9	305	1	234.887699	222.983003	-169.966006	1.965370e-08
XEC.8	592	17	233.875257	233.875257	-191.750513	1.054172e-03	*	*
XEC.24	11	17	233.201528	233.201528	-190.403057	5.367383e-04	*	*
KP.3.3	1715	1	232.968479	227.277504	-178.555008	1.441250e-06
XEC.19	59	17	230.227296	230.227296	-184.454592	2.739911e-05	*	*
XEC.29	135	17	230.104987	230.104987	-184.209974	2.430083e-05	*	*
XEC.32	42	17	226.488887	226.488887	-176.977773	6.541037e-07		*
XEC.4	192	17	225.813698	225.813698	-175.627397	3.330411e-07		*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2139_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5619_T|C, 6183_A|G, 6651_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15239_A|G, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18166_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21575_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28090_G|A, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28744_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): Japan/BRL25-0126/2025



Target: 5350 samples      Number of changes: 145                                             
BC: KP.3.1.1 + XEC.2      BC BR: 16-17                    BC BR coord: 6725 - 6726    
Direction L1: <<          Initial region span: 1-16,17-145 Gap history (edge excluded):
Alt. candidates: [], []                                                                             
Model 1BP/2BP comparison: 1BP vs 2BP: 1.25e-04                                                      
Rec. model vs L1: 3.40e-59 Rec. model vs L2: 1.51e-36                                         
Flags: Model_1BP_Best

KP.3.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.1	12013	16	13.453707	NaN	NaN	NaN	*	*	*
KP.3.1.12	39	4	11.473441	-33.806928	103.613855	2.987052e-21
KP.2.3	4440	15	10.689706	9.973545	16.052910	3.080741e-02	*	*
XEC.25	13	4	10.111699	-9.527962	55.055924	1.041697e-10
JN.1.68	34	4	8.021822	-27.964864	91.929728	1.026887e-18
KR.1.1	33	4	8.019008	-35.151576	106.303153	7.782457e-22
MM.1	35	4	7.993700	-27.961349	91.922699	1.032034e-18
JN.1.21	60	4	7.466884	-28.459178	92.918356	6.259603e-19
KP.2.3.12	62	4	7.450901	-28.491421	92.982842	6.074604e-19
JN.1.7.5	427	4	7.071349	-28.873509	93.747017	4.133468e-19

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	17	258.708890	NaN	NaN	NaN	*	*	*
XEC.14	193	17	234.560626	234.560626	-191.121253	3.249288e-11		*
XEC.2.1	265	32	233.050773	226.790232	-175.580464	1.371893e-14
XEC.25	13	32	231.353103	228.256642	-178.513284	5.936925e-14
XEC.36	30	17	229.431970	229.431970	-180.863940	1.922461e-13		*
XEC.30	135	12	228.578389	215.759121	-153.518241	2.223576e-19
XEC.2.2.1	46	32	227.987263	223.737566	-169.475131	6.497136e-16
XEC.18	165	17	227.715961	227.715961	-177.431922	3.459733e-14		*
XEC.8	592	12	225.968956	215.984782	-153.969565	2.784635e-19
XEC.39	155	17	225.561198	225.561198	-173.122397	4.009940e-15		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1102_C|T, 1267_C|T, 2060_G|A, 2790_C|T, 2937_C|T, 3037_C|T, 3431_G|T, 3466_T|C, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6720_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10576_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12488_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16650_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22003_A|T, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25916_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): Japan/BRL25-0174/2025



Target: 5350 samples       Number of changes: 145                                               
BC: XEC.15 + XEL.3         BC BR: 142-143                    BC BR coord: 28958 - 28959  
Direction L1: >>           Initial region span: 1-142,143-145 Gap history (edge excluded):
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 5.28e-09 Rec. model vs L2: 8.18e-101                                          
Flags: Model_2BP_Bad_L1_opp

XEC.15 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.15	127	142	243.035646	NaN	NaN	NaN	*	*	*
XEC.18	165	145	239.305318	234.515502	-163.031005	1.994394e-04	*
XEC.6	45	142	236.972112	236.972112	-167.944224	2.322758e-03	*	*
XEC.4	192	142	236.239126	236.239126	-166.478253	1.119358e-03	*	*
XEC.14	193	142	234.315089	234.315089	-162.630177	1.632872e-04	*	*
XEC.39	155	142	234.015280	234.015280	-162.030560	1.209661e-04	*	*
XEC.8	592	142	232.155677	232.155677	-158.311355	1.883112e-05	*	*
XEC.2	921	145	231.328886	228.827610	-151.655220	6.774026e-07
XEC.36	30	142	227.262810	227.262810	-148.525620	1.416368e-07		*
XEC.38	34	142	226.820595	226.820595	-147.641190	9.076428e-08		*

|||||

XEL.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEL.3	10	143	8.355316	NaN	NaN	NaN	*	*	*
XEL.4	10	143	8.355316	8.355316	-10.710631	1.000000	*	*
XEL.5	19	143	8.301248	8.301248	-10.602497	0.946485	*	*
LL.1	45	143	8.212215	8.212215	-10.424429	0.865022	*	*
BA.3	31	143	8.082593	8.082593	-10.165185	0.763379	*	*
JN.1.4.2	736	143	8.047264	8.047264	-10.094527	0.733447	*	*
BA.3.1	40	143	7.924533	7.924533	-9.849065	0.650509	*	*
XBB.1.5.54	21	143	7.795700	7.795700	-9.591400	0.571209	*	*
FL.14	29	143	7.660979	7.660979	-9.321957	0.499074	*	*
BE.5	231	143	7.550774	7.550774	-9.101548	0.447088	*	*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3430_A|G, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11956_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16332_C|T,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18804_C|T, 18894_C|T, 18962_C|A, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26176_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28009_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29311_C|T, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ247414



Target: 5350 samples      Number of changes: 143                                           
BC: XEC.36 + XEC.14       BC BR: 5-6                    BC BR coord: 1472 - 1473    
Direction L1: <<          Initial region span: 1-5,6-143 Gap history (edge excluded):
Alt. candidates: [], []                                                                           
Model 1BP/2BP comparison: 1BP vs 2BP: 1.02e-01                                                    
Rec. model vs L1: 2.37e-15 Rec. model vs L2: 1.55e-17                                       
Flags: Model_1BP_Best

XEC.36 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.36	30	5	12.056909	NaN	NaN	NaN	*	*	*
KP.4.2.4	22	5	10.642513	10.642513	-11.285026	0.244143	*	*
KP.4	35	5	9.713902	9.713902	-9.427804	0.096328	*	*
XEC.31	66	5	8.884757	8.884757	-7.769514	0.042004	*	*
LF.1.1.1	109	5	8.657713	8.657713	-7.315425	0.033541	*	*
KP.3.2.1	70	5	8.495540	8.495540	-6.991080	0.028439	*	*
LB.1.8	114	5	8.399290	8.399290	-6.798581	0.025861	*	*
KW.1.1	127	5	8.282270	8.282270	-6.564540	0.022937	*	*
JN.1.53	62	5	8.043243	8.043243	-6.086486	0.018133	*	*
MC.10	221	5	7.961161	7.961161	-5.922322	0.016656	*	*

|||||

XEC.14 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.14	193	6	246.955256	NaN	NaN	NaN	*	*	*
XEC.25	13	6	246.630563	246.630563	-187.261126	7.225274e-01	*	*
XEC.33	169	6	238.915123	238.915123	-171.830246	3.223090e-04	*	*
XEC.36	30	1	238.541006	226.484097	-146.968194	1.288226e-09
XEC.18	165	6	238.396306	238.396306	-170.792612	1.916193e-04	*	*
XEC.39	155	6	236.968445	236.968445	-167.936890	4.608606e-05	*	*
KP.3.3	1715	1	236.200410	231.098196	-156.196392	1.300951e-07
XEC.15	127	6	236.172759	236.172759	-166.345517	2.081160e-05	*	*
XEC.29	135	6	234.936926	234.936926	-163.873852	6.022549e-06		*
XEC.5	126	6	233.940272	233.940272	-161.880545	2.226677e-06		*

Target sequence

, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1471_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14119_C|T, 14408_C|T, 15267_A|G, 15668_A|C, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22002_A|T, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26151_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27792_27793, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ247419



Target: 5350 samples       Number of changes: 147                                                 
BC: XFB.3 + XEC.18         BC BR: 6-7                     BC BR coord: 896 - 897           
Direction L1: <<           Initial region span: 1-6,10-147 Gap history (edge excluded): 6-10
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  -                                                                             
Rec. model vs L1: 4.01e-208 Rec. model vs L2: 8.23e-09                                             
Flags: Model_2BP_Bad_L1_opp

XFB.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFB.3	56	6	13.391693	NaN	NaN	NaN	*	*	*
KP.2.28.1	10	6	13.318834	13.318834	-14.637668	0.932394	*	*
PG.3	31	6	13.219092	13.219092	-14.438183	0.843665	*	*
KS.1.1	52	6	12.128262	12.128262	-12.256524	0.283654	*	*
BA.2.86	38	6	11.790418	11.790418	-11.580836	0.201897	*	*
MU.1	173	6	11.716817	11.716817	-11.433633	0.187308	*	*
KP.3.1.10	51	6	11.585726	11.585726	-11.171452	0.164474	*	*
XFG.1	14	6	11.498487	11.498487	-10.996974	0.151072	*	*
ML.2	67	6	11.494581	11.494581	-10.989162	0.150318	*	*
KP.2.14	169	6	11.461630	11.461630	-10.923260	0.145148	*	*

|||||

XEC.18 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.18	165	10	240.561198	NaN	NaN	NaN	*	*	*
XEC.2	921	9	236.972216	216.972216	-125.944432	5.170273e-05	*	*
XEC.4	192	8	235.278602	225.278602	-142.557204	2.101361e-01	*
KP.3.3	1715	10	229.721022	211.450626	-114.901253	2.071133e-07		*
XEC.14	193	10	229.647497	215.933898	-123.867796	1.836617e-05	*	*
XEC.5	126	10	228.135490	214.421891	-120.843782	4.037035e-06		*
XEC.32	42	10	228.130308	214.416709	-120.833417	4.016900e-06		*
XEC.25	13	10	227.591618	213.878019	-119.756038	2.352575e-06		*
XEC.40	52	10	226.203093	204.852785	-101.705569	2.831626e-10		*
XEC.9	305	18	226.158126	210.388808	-112.777615	7.175560e-08

Target sequence

, 21_C|T, 44_C|T, 222_C|T, 241_C|T, 670_T|G, 897_C|A, 1959_C|T, 2060_G|A, 2445_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6027_C|T, 6183_A|G, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10171_A|G, 10198_C|T, 10369_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18761_T|C, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20670_G|A, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21635_21643, 21711_C|T, 21738_T|C, 21765_21770, 21938_G|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T,
25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ247681



Target: 5350 samples       Number of changes: 146                                               
BC: XEC.8 + LF.4           BC BR: 143-144                    BC BR coord: 28958 - 28959  
Direction L1: >>           Initial region span: 1-143,144-146 Gap history (edge excluded):
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 5.20e-09 Rec. model vs L2: 2.73e-106                                          
Flags: Model_2BP_Bad_L1_opp

XEC.8 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.8	592	143	238.622056	NaN	NaN	NaN	*	*	*
XEC.9	305	143	231.685222	231.685222	-149.370444	9.731231e-04	*	*
XEC.18	165	143	230.691897	230.691897	-147.383793	3.597864e-04	*	*
XEC.2	921	143	227.962222	227.962222	-141.924445	2.346501e-05	*	*
XEC.5	126	143	223.670048	223.670048	-133.340096	3.215863e-07		*
XEC.6	45	143	223.380486	223.380486	-132.760973	2.406313e-07		*
XEC.14	193	143	221.996638	221.996638	-129.993277	6.023574e-08		*
KP.3.3	1715	143	219.297734	219.297734	-124.595468	4.068465e-09		*
XEC.32	42	143	217.295479	217.295479	-120.590957	5.478607e-10		*
XEC.33	169	143	217.160740	217.160740	-120.321479	4.786746e-10		*

|||||

LF.4 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.4	38	144	9.420716	NaN	NaN	NaN	*	*	*
LF.4.1	50	144	9.412908	9.412908	-12.825815	0.995012	*	*
LF.9	48	144	7.500702	7.500702	-9.001404	0.146607	*	*
CH.1.1.7	39	144	7.117473	7.117473	-8.234946	0.099759	*	*
PF.1	19	144	6.476277	6.476277	-6.952554	0.052602	*	*
MC.1.3	51	144	5.439773	5.439773	-4.879546	0.018686	*	*
BA.5.2.37	108	144	4.587857	4.587857	-3.175715	0.007987	*	*
XBB.1.5.4	683	144	4.155477	4.155477	-2.310954	0.005169	*	*
LB.1.2	199	144	3.950768	3.950768	-1.901537	0.004211	*	*
XBB.1.5.17	1117	144	3.439656	3.439656	-0.879311	0.002529	*	*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3179_G|A, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5884_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15240_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 17676_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19018_C|T, 19716_C|T, 19806_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24821_G|T, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25186_G|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29427_G|A, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ247716



Target: 5350 samples      Number of changes: 147                                                   
BC: XEC.30 + XEC.2        BC BR: 17-18                    BC BR coord: 7842 - 7843          
Direction L1: <<          Initial region span: 1-15,21-147 Gap history (edge excluded): 15-21
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 8.48e-01                                                            
Rec. model vs L1: 3.41e-20 Rec. model vs L2: 2.42e-19                                               
Flags: Model_1BP_Best

XEC.30 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.30	135	15	21.876803	NaN	NaN	NaN	*	*	*
KP.3.3	1715	19	21.168534	15.731465	10.537071	1.284025e+00	*
XEC.35.1	28	13	17.890032	5.102766	31.794468	3.120288e-05	*
XEC.23	142	13	17.704623	-0.170696	42.341391	1.596950e-07
XEC.4.7	13	13	17.629701	-4.145893	50.291787	2.998961e-09
XEC.17	13	13	16.675670	3.888404	34.223192	9.258208e-06
XEC.15	127	13	16.658880	3.863709	34.272583	9.029622e-06
XEC.4	192	13	16.214163	3.426897	35.146206	5.815406e-06
XEC.38	34	13	16.166447	3.379182	35.241637	5.559513e-06
XEC.5	126	13	16.154980	3.367714	35.264572	5.504195e-06

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	21	246.901961	NaN	NaN	NaN	*	*	*
XEC.30	135	7	235.757938	218.709128	-165.418257	5.465393e-11
XEC.29	135	21	230.812321	226.249974	-180.499947	1.028494e-07		*
XEK.5	28	21	230.675425	219.714658	-167.429317	1.493095e-10		*
XEC.8	592	21	221.359337	216.796990	-161.593980	8.052810e-12		*
KP.3.3	1715	7	220.898240	204.478298	-136.956595	3.610862e-17
XEC.40	52	21	220.694371	216.112605	-160.225211	4.079690e-12		*
XEC.9	305	21	219.695064	215.132717	-158.265434	1.531153e-12		*
XEC.14	193	21	219.054517	214.492169	-156.984339	8.033387e-13		*
XEC.19	59	21	218.239112	213.676764	-155.353529	3.555893e-13		*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1919_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5784_C|T, 6183_A|G, 6238_T|C, 7842_A|G, 8293_C|T, 8393_G|A,
8482_T|C, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12514_G|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24910_T|C, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27005_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28113_A|G, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29614_C|T, 29734_29759

 Case 72 (XEC): OZ247800



Target: 5350 samples       Number of changes: 143                                           
BC: KP.2.3.10 + XEC.14     BC BR: 6-7                    BC BR coord: 1701 - 1702    
Direction L1: <<           Initial region span: 1-6,7-143 Gap history (edge excluded):
Alt. candidates: [], []                                                                            
Model 1BP/2BP comparison:  1BP vs 2BP: 2.23e-01                                                    
Rec. model vs L1: 5.66e-148 Rec. model vs L2: 2.58e-17                                       
Flags: Model_1BP_Best

KP.2.3.10 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3.10	10	6	17.073087	NaN	NaN	NaN	*	*	*
KP.3.2.8	26	6	14.349653	14.349653	-16.699307	6.554620e-02	*	*
KP.3.1.9	26	6	13.002580	13.002580	-14.005159	1.707739e-02	*	*
JN.1.18	431	6	11.935967	11.935967	-11.871935	5.857690e-03	*	*
LF.7.9.3	20	5	11.825673	1.825673	8.348653	2.382370e-07		*
XFB.3	56	5	11.670112	1.670112	8.659776	2.040298e-07		*
XEL.5	19	5	11.593891	1.593891	8.812218	1.892873e-07		*
JN.1.7.2	180	6	11.330096	11.330096	-10.660192	3.198735e-03	*	*
LC.1	10	5	11.297148	1.297148	9.405704	1.402275e-07		*
XEC.35.1	28	5	11.252812	1.252812	9.494375	1.347291e-07		*

|||||

XEC.14 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.14	193	7	223.925313	NaN	NaN	NaN	*	*	*
XEC.38	34	7	220.257510	220.257510	-144.515020	2.560417e-02	*	*
XEC.4	192	7	219.806277	219.806277	-143.612555	1.624451e-02	*	*
XEC.9	305	7	218.566509	218.566509	-141.133019	4.700906e-03	*	*
XEC.6	45	7	216.614248	216.614248	-137.228496	6.688171e-04	*	*
XEC.8	592	7	216.184348	216.184348	-136.368696	4.350716e-04	*	*
XEC.30	135	7	215.540663	215.540663	-135.081326	2.282658e-04	*	*
MC.24.1	25	7	214.884070	214.884070	-133.768140	1.185708e-04	*	*
XEC.18	165	7	214.665222	214.665222	-133.330443	9.515533e-05	*	*
XEC.2	921	13	214.265019	199.631724	-103.263449	2.810707e-11

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1686_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11461_C|T, 11727_G|A, 12394_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16200_T|C,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21859_C|A, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25538_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27047_G|A, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ249457



Target: 5350 samples       Number of changes: 136                                                   
BC: XEC.32 + XEC.2         BC BR: 14-15                    BC BR coord: 7842 - 7843          
Direction L1: <<           Initial region span: 1-14,18-136 Gap history (edge excluded): 14-18
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 2.60e-33 Rec. model vs L2: 3.03e-25                                               
Flags: Model_2BP_Bad_L1_opp

XEC.32 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.32	42	14	23.490995	NaN	NaN	NaN	*	*	*
XEC.8.1	12	13	19.955191	18.143349	-0.286697	4.771951e-03	*	*
KP.3.1.1	12013	16	19.079354	16.491100	3.017799	9.118820e-04	*
JN.1	17255	17	15.450465	11.922416	12.155168	9.445237e-06
XEC.25	13	12	15.079158	8.682101	18.635797	3.699123e-07
XEC.18.3	13	12	15.079158	8.682101	18.635797	3.699123e-07
XEC.16	23	12	15.079158	8.682101	18.635797	3.699123e-07
XEC.4.3	10	12	15.079158	-7.384864	50.769728	3.900838e-14
XEC.17	13	12	15.079158	8.682101	18.635797	3.699123e-07
XEC.24	11	12	15.079158	8.682101	18.635797	3.699123e-07

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	18	183.586092	NaN	NaN	NaN	*	*	*
KP.3.3	1715	3	171.436813	161.767818	-43.535636	1.557521e-07
XEC.8	592	3	165.653783	147.099895	-14.199791	6.627259e-14
XEC.18	165	23	160.038268	138.708116	2.583767	1.505231e-17
XEC.19	59	23	158.923365	137.593213	4.813573	4.935883e-18
XEC.14	193	23	156.439818	135.109667	9.780667	4.112852e-19
XEC.2.2.1	46	21	153.193672	133.112240	13.775519	5.566140e-20
XEC.36	30	23	152.571772	131.241621	17.516757	8.578739e-21
XEC.11	16	23	152.566485	131.236333	17.527333	8.535953e-21
XEC.2.2	273	21	151.947393	131.918804	16.162392	1.693338e-20

Target sequence

, 241_C|T, 295_G|A, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7081_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8299_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 9733_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18499_T|C, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20404_C|T, 21711_C|T, 21738_T|C, 21812_C|A, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C,
22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C,
22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24130_C|T, 24378_C|T, 24424_A|T, 24469_T|A,
24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26319_A|G, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29253_C|T, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ249462



Target: 5350 samples       Number of changes: 146                                               
BC: XEC.8 + LF.4           BC BR: 143-144                    BC BR coord: 28958 - 28959  
Direction L1: >>           Initial region span: 1-143,144-146 Gap history (edge excluded):
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 5.17e-09 Rec. model vs L2: 9.13e-107                                          
Flags: Model_2BP_Bad_L1_opp

XEC.8 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.8	592	143	237.747480	NaN	NaN	NaN	*	*	*
XEC.18	165	143	234.203584	234.203584	-156.407168	2.901333e-02	*	*
XEC.9	305	143	231.050766	231.050766	-150.101532	1.237082e-03	*	*
XEC.2	921	143	227.803631	227.803631	-143.607263	4.820730e-05	*	*
XEC.11	16	143	225.053248	225.053248	-138.106496	3.081790e-06		*
XEC.19	59	143	223.566694	223.566694	-135.133389	6.945512e-07		*
XEC.6	45	143	223.091103	223.091103	-134.182207	4.319310e-07		*
XEC.5	126	143	222.580647	222.580647	-133.161293	2.593727e-07		*
XEC.32	42	143	222.487319	222.487319	-132.974638	2.358665e-07		*
XEC.14	193	143	221.640518	221.640518	-131.281037	1.013182e-07		*

|||||

LF.4 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.4	38	144	9.420716	NaN	NaN	NaN	*	*	*
LF.4.1	50	144	9.412908	9.412908	-12.825815	0.995012	*	*
LF.9	48	144	7.500702	7.500702	-9.001404	0.146607	*	*
CH.1.1.7	39	144	7.117473	7.117473	-8.234946	0.099759	*	*
PF.1	19	144	6.476277	6.476277	-6.952554	0.052602	*	*
MC.1.3	51	144	5.439773	5.439773	-4.879546	0.018686	*	*
BA.5.2.37	108	144	4.587857	4.587857	-3.175715	0.007987	*	*
XBB.1.5.4	683	144	4.155477	4.155477	-2.310954	0.005169	*	*
LB.1.2	199	144	3.950768	3.950768	-1.901537	0.004211	*	*
XBB.1.5.17	1117	144	3.439656	3.439656	-0.879311	0.002529	*	*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3179_G|A, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5884_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15240_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 17676_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19018_C|T, 19716_C|T, 19806_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24821_G|T, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25186_G|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29427_G|A, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ249475



Target: 5350 samples      Number of changes: 144                                                 
BC: XEC.4.3 + XEC.2       BC BR: 11-12                   BC BR coord: 4387 - 4388         
Direction L1: <<          Initial region span: 1-8,12-144 Gap history (edge excluded): 8-12
Alt. candidates: [], []                                                                                 
Model 1BP/2BP comparison: 1BP vs 2BP: 2.61e-06                                                          
Rec. model vs L1: 2.67e-45 Rec. model vs L2: 1.07e-17                                             
Flags: Model_1BP_Best

XEC.4.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4.3	10	8	19.322509	NaN	NaN	NaN	*	*	*
XEC.25	13	8	19.322509	11.469367	-0.938735	1.0	*	*
XEC.32	42	8	19.322509	11.469367	-0.938735	1.0	*	*
XEC.8.1	12	8	19.322509	11.469367	-0.938735	1.0	*	*
XEC.18.3	13	8	19.322509	11.469367	-0.938735	1.0	*	*
XEC.4.1.4	23	8	19.322509	11.469367	-0.938735	1.0	*	*
XEC.16	23	8	19.322509	11.469367	-0.938735	1.0	*	*
XEC.17	13	8	19.322509	11.469367	-0.938735	1.0	*	*
XEC.24	11	8	19.322509	11.469367	-0.938735	1.0	*	*
XEC.22	23	8	19.322509	11.469367	-0.938735	1.0	*	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	12	265.769700	NaN	NaN	NaN	*	*	*
XEC.2.2	273	12	240.387585	240.387585	-194.775169	9.497429e-12		*
XEC.8	592	1	240.308765	228.961356	-171.922711	1.031858e-16
XEC.33	169	1	236.834593	225.437197	-164.874394	3.039010e-18
KP.3.3	1715	1	236.282739	229.445069	-172.890138	1.675919e-16
XEC.14	193	3	236.121775	225.780481	-165.560963	4.291051e-18
XEC.9	305	1	230.573627	219.187445	-152.374889	5.866669e-21
XEC.31	66	1	225.493343	221.992796	-157.985593	9.744489e-20
XEC.2.1	265	13	224.451157	214.451157	-142.902314	5.152372e-23		*
XEC.15	127	1	222.740260	211.368779	-136.737558	2.367992e-24

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3914_G|A, 4184_G|A, 4321_C|T, 5178_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11866_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 17795_C|T,
18084_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20405_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29020_A|G, 29353_C|T, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ249692



Target: 5350 samples       Number of changes: 145                                               
BC: XEC.8 + LF.4           BC BR: 142-143                    BC BR coord: 28958 - 28959  
Direction L1: >>           Initial region span: 1-142,143-145 Gap history (edge excluded):
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 5.17e-09 Rec. model vs L2: 4.09e-106                                          
Flags: Model_2BP_Bad_L1_opp

XEC.8 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.8	592	142	241.280891	NaN	NaN	NaN	*	*	*
XEC.9	305	142	234.806936	234.806936	-159.613871	1.541499e-03	*	*
XEC.18	165	142	233.998499	233.998499	-157.996998	6.891856e-04	*	*
XEC.2	921	142	231.443793	231.443793	-152.887587	5.354436e-05	*	*
XEC.6	45	142	226.502137	226.502137	-143.004274	3.811778e-07		*
XEC.5	126	142	226.202825	226.202825	-142.405649	2.837989e-07		*
XEC.14	193	142	225.194061	225.194061	-140.388122	1.033649e-07		*
XEC.32	42	142	222.757859	222.757859	-135.515719	9.054536e-09		*
KP.3.3	1715	142	221.914177	221.914177	-133.828354	3.889443e-09		*
XEC.33	169	142	220.912909	220.912909	-131.825818	1.430846e-09		*

|||||

LF.4 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.4	38	143	9.420716	NaN	NaN	NaN	*	*	*
LF.4.1	50	143	9.412908	9.412908	-12.825815	0.995012	*	*
LF.9	48	143	7.500702	7.500702	-9.001404	0.146607	*	*
CH.1.1.7	39	143	7.117473	7.117473	-8.234946	0.099759	*	*
PF.1	19	143	6.476277	6.476277	-6.952554	0.052602	*	*
MC.1.3	51	143	5.439773	5.439773	-4.879546	0.018686	*	*
BA.5.2.37	108	143	4.587857	4.587857	-3.175715	0.007987	*	*
XBB.1.5.4	683	143	4.155477	4.155477	-2.310954	0.005169	*	*
LB.1.2	199	143	3.950768	3.950768	-1.901537	0.004211	*	*
XBB.1.5.17	1117	143	3.439656	3.439656	-0.879311	0.002529	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3179_G|A, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5884_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15240_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 17676_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19018_C|T, 19716_C|T, 19806_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24821_G|T, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25186_G|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29427_G|A, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ249699



Target: 5350 samples       Number of changes: 135                                                   
BC: XEC.32 + XEC.2         BC BR: 14-15                    BC BR coord: 7842 - 7843          
Direction L1: <<           Initial region span: 1-14,18-135 Gap history (edge excluded): 14-18
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 2.56e-33 Rec. model vs L2: 3.03e-25                                               
Flags: Model_2BP_Bad_L1_opp

XEC.32 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.32	42	14	23.490995	NaN	NaN	NaN	*	*	*
XEC.8.1	12	13	19.955191	18.143349	-0.286697	4.771951e-03	*	*
KP.3.1.1	12013	16	19.079354	16.491100	3.017799	9.118820e-04	*
JN.1	17255	17	15.450465	11.922416	12.155168	9.445237e-06
XEC.25	13	12	15.079158	8.682101	18.635797	3.699123e-07
XEC.18.3	13	12	15.079158	8.682101	18.635797	3.699123e-07
XEC.16	23	12	15.079158	8.682101	18.635797	3.699123e-07
XEC.4.3	10	12	15.079158	-7.384864	50.769728	3.900838e-14
XEC.17	13	12	15.079158	8.682101	18.635797	3.699123e-07
XEC.24	11	12	15.079158	8.682101	18.635797	3.699123e-07

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	18	180.051805	NaN	NaN	NaN	*	*	*
KP.3.3	1715	3	167.916458	158.247464	-36.494927	1.573175e-07
XEC.8	592	3	162.113193	143.559305	-7.118611	6.594205e-14
XEC.18	165	23	156.527608	135.197456	9.605087	1.535639e-17
XEC.19	59	23	155.376006	134.045855	11.908289	4.862398e-18
XEC.14	193	23	152.913293	131.583142	16.833716	4.154187e-19
XEC.2.2.1	46	21	149.690271	129.608840	20.782320	5.764405e-20
XEC.36	30	23	149.162400	127.832249	24.335502	9.720985e-21
XEC.11	16	23	149.019126	127.688975	24.622050	8.451018e-21
XEC.2.2	273	21	148.407374	128.378785	23.242430	1.684893e-20

Target sequence

, 241_C|T, 295_G|A, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7081_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8299_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 9733_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18499_T|C, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20404_C|T, 21711_C|T, 21738_T|C, 21812_C|A, 21941_G|T, 21987_G|A, 22032_T|C, 22033_C|A,
22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T,
22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24130_C|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T,
24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26319_A|G, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29253_C|T, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ249708



Target: 5350 samples       Number of changes: 146                                               
BC: XEC.8 + LF.4           BC BR: 143-144                    BC BR coord: 28958 - 28959  
Direction L1: >>           Initial region span: 1-143,144-146 Gap history (edge excluded):
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 5.17e-09 Rec. model vs L2: 9.89e-107                                          
Flags: Model_2BP_Bad_L1_opp

XEC.8 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.8	592	143	237.685831	NaN	NaN	NaN	*	*	*
XEC.18	165	143	234.195624	234.195624	-156.391248	3.050087e-02	*	*
XEC.9	305	143	231.170660	231.170660	-150.341319	1.481056e-03	*	*
XEC.2	921	143	227.791937	227.791937	-143.583873	5.042618e-05	*	*
XEC.11	16	143	225.357131	225.357131	-138.714262	4.417220e-06		*
XEC.19	59	143	223.550187	223.550187	-135.100374	7.265199e-07		*
XEC.6	45	143	223.208806	223.208806	-134.417611	5.171153e-07		*
XEC.5	126	143	222.598328	222.598328	-133.196656	2.809750e-07		*
XEC.32	42	143	222.505001	222.505001	-133.010001	2.555111e-07		*
XEC.14	193	143	221.669661	221.669661	-131.339323	1.108597e-07		*

|||||

LF.4 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.4	38	144	9.420716	NaN	NaN	NaN	*	*	*
LF.4.1	50	144	9.412908	9.412908	-12.825815	0.995012	*	*
LF.9	48	144	7.500702	7.500702	-9.001404	0.146607	*	*
CH.1.1.7	39	144	7.117473	7.117473	-8.234946	0.099759	*	*
PF.1	19	144	6.476277	6.476277	-6.952554	0.052602	*	*
MC.1.3	51	144	5.439773	5.439773	-4.879546	0.018686	*	*
BA.5.2.37	108	144	4.587857	4.587857	-3.175715	0.007987	*	*
XBB.1.5.4	683	144	4.155477	4.155477	-2.310954	0.005169	*	*
LB.1.2	199	144	3.950768	3.950768	-1.901537	0.004211	*	*
XBB.1.5.17	1117	144	3.439656	3.439656	-0.879311	0.002529	*	*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3179_G|A, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5884_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15240_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 17676_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19018_C|T, 19716_C|T, 19806_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24821_G|T, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25186_G|T, 25207_C|T, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29427_G|A, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ249750



Target: 5350 samples       Number of changes: 147                                               
BC: XEC.8 + LF.4           BC BR: 144-145                    BC BR coord: 28958 - 28959  
Direction L1: >>           Initial region span: 1-144,145-147 Gap history (edge excluded):
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 5.20e-09 Rec. model vs L2: 3.56e-106                                          
Flags: Model_2BP_Bad_L1_opp

XEC.8 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.8	592	144	245.806625	NaN	NaN	NaN	*	*	*
XEC.9	305	144	238.969082	238.969082	-163.938164	1.075467e-03	*	*
XEC.18	165	144	238.014630	238.014630	-162.029260	4.138529e-04	*	*
XEC.2	921	144	235.155612	235.155612	-156.311225	2.370084e-05	*	*
XEC.5	126	144	230.952438	230.952438	-147.904877	3.536352e-07		*
XEC.6	45	144	230.642080	230.642080	-147.284159	2.593727e-07		*
XEC.14	193	144	229.248604	229.248604	-144.497208	6.460332e-08		*
KP.3.3	1715	144	226.545771	226.545771	-139.091542	4.320045e-09		*
XEC.32	42	144	224.743253	224.743253	-135.486505	7.140986e-10		*
XEC.33	169	144	224.356609	224.356609	-134.713217	4.834854e-10		*

|||||

LF.4 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.4	38	145	9.420716	NaN	NaN	NaN	*	*	*
LF.4.1	50	145	9.412908	9.412908	-12.825815	0.995012	*	*
LF.9	48	145	7.500702	7.500702	-9.001404	0.146607	*	*
CH.1.1.7	39	145	7.117473	7.117473	-8.234946	0.099759	*	*
PF.1	19	145	6.476277	6.476277	-6.952554	0.052602	*	*
MC.1.3	51	145	5.439773	5.439773	-4.879546	0.018686	*	*
BA.5.2.37	108	145	4.587857	4.587857	-3.175715	0.007987	*	*
XBB.1.5.4	683	145	4.155477	4.155477	-2.310954	0.005169	*	*
LB.1.2	199	145	3.950768	3.950768	-1.901537	0.004211	*	*
XBB.1.5.17	1117	145	3.439656	3.439656	-0.879311	0.002529	*	*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3179_G|A, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5884_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15240_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 17676_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19018_C|T, 19716_C|T, 19806_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24821_G|T, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25186_G|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29427_G|A, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ252346



Target: 5350 samples      Number of changes: 145                                                 
BC: KP.3.3 + XEC.30       BC BR: 8-9                     BC BR coord: 2060 - 2061         
Direction L1: <<          Initial region span: 1-8,10-145 Gap history (edge excluded): 8-10
Alt. candidates: [], []                                                                                 
Model 1BP/2BP comparison: 1BP vs 2BP: 1.50e-01                                                          
Rec. model vs L1: 4.35e-23 Rec. model vs L2: 1.08e-10                                             
Flags: Model_1BP_Best

KP.3.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.3	1715	8	13.882190	NaN	NaN	NaN	*	*	*
XEC.17	13	8	9.973636	9.973636	4.052727	2.014095e-02	*	*
JN.1	17255	7	8.909044	-1.090956	26.181912	3.152184e-07		*
KP.3.1.1	12013	7	8.902425	5.795081	12.409837	3.081265e-04	*	*
XEC.29	135	8	7.818912	7.818912	8.362177	2.334401e-03	*	*
LF.7.9.3	20	3	7.111420	-18.174327	60.348653	1.198644e-14
XFB.3	56	3	6.955858	-18.329888	60.659776	1.026537e-14
NY.12.1	17	3	6.912387	-36.265998	96.531996	1.668412e-22
XEL.5	19	3	6.879637	-29.632125	83.264250	1.270127e-19
MC.13.2.4	37	3	6.742160	-26.379166	76.758332	3.275700e-18

|||||

XEC.30 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.30	135	10	251.173011	NaN	NaN	NaN	*	*	*
XEC.14	193	10	244.536353	234.536353	-173.072705	1.307027e-03	*	*
XEC.2	921	17	244.451479	227.052361	-158.104723	7.338215e-07
XEC.9	305	18	241.134674	229.078955	-162.157909	5.587380e-06
XEC.40	52	10	240.941351	223.304642	-150.609284	1.734433e-08		*
XEC.18	165	10	239.301526	229.301526	-162.603052	6.962305e-06		*
XEC.6	45	10	238.641398	228.641398	-161.282797	3.598476e-06		*
XEC.39	155	10	238.510654	228.510654	-161.021308	3.159806e-06		*
XEC.17	13	5	238.147982	223.385214	-150.770428	1.878889e-08
XEC.31	66	28	237.758381	217.468768	-138.937537	5.070483e-11

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 505_T|C, 670_T|G, 897_C|A, 934_C|T, 2060_G|A, 2504_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6023_T|C, 6183_A|G, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 9995_T|G, 10029_C|T, 10198_C|T, 10369_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C,
14123_G|A, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27198_A|G, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ252347



Target: 5350 samples      Number of changes: 144                                                   
BC: KP.3.3 + XEC.2        BC BR: 16-17                    BC BR coord: 4387 - 4388          
Direction L1: <<          Initial region span: 1-16,18-144 Gap history (edge excluded): 16-18
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 2.36e-05                                                            
Rec. model vs L1: 1.51e-17 Rec. model vs L2: 5.74e-22                                               
Flags: Model_1BP_Best

KP.3.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.3	1715	16	12.726113	NaN	NaN	NaN	*	*	*
KP.2.3.2	28	4	10.921530	-14.010545	62.021089	2.449836e-12
JN.1.11	43	4	10.145369	-14.868558	63.737115	1.036678e-12
KP.2.3	4440	7	10.132628	9.468492	15.063016	3.858082e-02	*
LF.7.1	165	4	9.226868	-15.643625	65.287249	4.776014e-13
JN.1.4.5	1757	6	8.072072	-4.415975	42.831951	3.599089e-08
JN.1	17255	7	7.743457	5.044672	23.910656	4.619749e-04	*
LF.7.9.3	20	3	7.111420	-27.933323	89.866646	2.195768e-18
MC.24	831	4	7.069973	2.141111	29.717778	2.529257e-05	*
XFB.3	56	3	6.955858	-27.939849	89.879698	2.184816e-18

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	18	243.046368	NaN	NaN	NaN	*	*	*
XEC.4	192	18	232.046389	222.046389	-158.092777	1.670170e-05	*	*
XEC.29	135	19	225.501038	205.113930	-124.227859	7.415751e-13		*
KP.3.3	1715	6	225.237159	208.483904	-130.967809	2.156391e-11
XEC.9	305	19	221.541225	209.068200	-132.136401	3.870703e-11		*
XEC.13	30	18	218.276296	208.276296	-130.552592	1.747937e-11		*
XEC.2.2.1	46	18	217.929696	207.929696	-129.859392	1.237924e-11		*
XEC.39	155	6	216.164865	203.719601	-121.439202	1.837868e-13
XEC.8	592	18	215.072311	205.072311	-124.144621	7.089439e-13		*
XEC.14	193	7	214.703812	203.549114	-121.098227	1.550545e-13

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 547_C|T, 616_T|C, 670_T|G, 897_C|A, 936_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3602_C|T, 4184_G|A, 4321_C|T, 5192_C|A, 6183_A|G, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18131_C|T, 18163_A|G, 18488_T|C, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20451_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25162_C|T, 25207_C|T, 25521_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ252376



Target: 5350 samples       Number of changes: 142                                           
BC: XFG.3 + XEC.17         BC BR: 8-9                    BC BR coord: 899 - 900      
Direction L1: <<           Initial region span: 1-8,9-142 Gap history (edge excluded):
Alt. candidates: [], []                                                                            
Model 1BP/2BP comparison:  1BP vs 2BP: 2.15e-03                                                    
Rec. model vs L1: 2.89e-244 Rec. model vs L2: 4.34e-11                                       
Flags: Model_1BP_Best

XFG.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFG.3	480	8	14.594840	NaN	NaN	NaN	*	*	*
KS.1.1.2	252	7	10.984879	0.984879	14.030243	1.228152e-06		*
BA.2.86.1	1343	8	10.710812	10.710812	-5.421625	2.054783e-02	*	*
MC.35	258	7	10.586893	0.586893	14.826214	8.232549e-07		*
KP.3.1.4	511	7	10.375968	0.375968	15.248065	6.673174e-07		*
MC.16	917	7	8.838234	-1.161766	18.323532	1.437773e-07		*
XEC.17	13	4	8.775898	-6.509849	29.019697	6.826765e-10
KP.3.1.1	12013	8	8.745007	8.745007	-1.490014	2.879899e-03	*	*
JN.1.64.1	14	4	8.594396	-6.999652	29.999304	4.182256e-10
KP.2.2	1334	7	8.324334	-1.675666	19.351332	8.590704e-08		*

|||||

XEC.17 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.17	13	9	236.871490	NaN	NaN	NaN	*	*	*
XEC.14	193	9	224.706822	224.706822	-155.413644	5.209639e-06		*
XEC.38	34	9	221.024500	221.024500	-148.048999	1.314026e-07		*
XEC.4	192	9	220.545730	220.545730	-147.091460	8.130974e-08		*
XEC.9	305	9	219.306120	219.306120	-144.612240	2.352976e-08		*
XEC.6	45	9	217.413891	217.413891	-140.827781	3.554683e-09		*
XEC.8	592	9	217.052861	217.052861	-140.105722	2.480018e-09		*
XEC.30	135	9	216.454556	216.454556	-138.909111	1.361063e-09		*
MC.24.1	25	9	215.662274	215.662274	-137.324548	6.146304e-10		*
XEC.18	165	9	215.374343	215.374343	-136.748686	4.622108e-10		*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 583_C|T, 635_C|T, 670_T|G, 897_C|A, 898_T|C, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 8664_C|T, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17097_T|C,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21764_21769, 21770_G|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27580_27616, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ252580



Target: 5350 samples       Number of changes: 136                                                   
BC: XEC.4 + XEC.2          BC BR: 13-14                    BC BR coord: 7842 - 7843          
Direction L1: <<           Initial region span: 1-11,16-136 Gap history (edge excluded): 11-16
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 8.72e-35 Rec. model vs L2: 2.21e-24                                               
Flags: Model_2BP_Bad_L1_opp

XEC.4 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4	192	11	19.610508	NaN	NaN	NaN	*	*	*
XEC.18	165	11	19.042211	12.639075	16.721849	5.627049e-01	*	*
XEC.8	592	11	17.718321	11.319573	19.360853	1.503183e-01	*	*
KP.3.3	1715	11	12.126020	1.352704	39.294593	7.067526e-06		*
XEC.18.2	10	11	11.417667	5.020611	31.958779	2.760303e-04	*	*
XEC.1	99	11	9.617396	3.220339	35.559322	4.562750e-05	*	*
KP.3.1	1957	11	8.991071	-1.791261	45.582522	3.043766e-07		*
PY.4	10	4	8.702742	-21.103047	84.206093	1.244553e-15
KP.2.14.1	13	4	8.545738	-20.598457	83.196914	2.062206e-15
JN.1	17255	15	8.256835	4.333642	33.332716	1.391442e-04	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	16	200.197467	NaN	NaN	NaN	*	*	*
XEC.8	592	1	183.352989	172.033415	-66.066831	3.690828e-10
XEC.19	59	16	183.286016	176.841610	-75.683220	4.507221e-08		*
KP.3.3	1715	16	180.051973	173.607567	-69.215134	1.782944e-09		*
XEC.30	135	3	177.558874	166.187766	-54.375532	1.068249e-12
XEC.39	155	3	172.777755	161.416302	-44.832604	9.013977e-15
XEC.9	305	16	170.975963	164.531558	-51.063115	2.031158e-13		*
XEC.14	193	4	170.973367	160.710989	-43.421978	4.453883e-15
XEC.2.2.1	46	19	167.697041	157.615610	-37.231220	2.016496e-16
XEC.18	165	1	166.650980	154.011905	-30.023810	5.482338e-18

Target sequence

, 241_C|T, 635_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 6183_A|G, 6406_C|T, 7842_A|G, 8293_C|T, 8299_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 14790_C|T, 15126_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20404_C|T, 21641_G|T, 21711_C|T, 21738_T|C, 21765_21770, 21812_C|A, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C,
22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C,
22813_G|T, 22879_C|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C,
23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28254, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ253886



Target: 5350 samples      Number of changes: 148                                                   
BC: XEC.11 + XEC.2        BC BR: 16-17                    BC BR coord: 6183 - 6184          
Direction L1: <<          Initial region span: 1-12,19-148 Gap history (edge excluded): 12-19
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 2.55e-06                                                            
Rec. model vs L1: 3.03e-27 Rec. model vs L2: 8.21e-27                                               
Flags: Model_1BP_Best

XEC.11 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.11	16	12	29.383520	NaN	NaN	NaN	*	*	*
XEC.11.1	166	12	29.170127	15.722473	6.555054	8.108602e-05	*	*
KP.3.3	1715	16	18.687254	18.687254	0.625492	1.572639e-03	*
XEC.11.1.1	12	12	18.317398	4.875786	28.248427	1.581329e-09		*
XEC.35.1	28	12	17.918241	13.674890	10.650221	1.049092e-05	*	*
XEC.14	193	12	16.252217	12.008866	13.982268	1.984785e-06		*
XEC.13	30	17	16.162531	10.955762	16.088475	6.910871e-07
XEC.24.1	18	12	15.861852	11.561343	14.877315	1.265555e-06		*
XEC.23	142	12	15.686687	6.355283	25.289433	6.946694e-09		*
XEC.38	34	12	15.577978	11.334627	15.330746	1.010566e-06		*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	19	218.384527	NaN	NaN	NaN	*	*	*
XEC.33	169	52	208.145394	188.073475	-88.146951	4.586401e-07
KP.3.3	1715	19	206.180018	181.803758	-75.607517	8.678519e-10		*
XEC.13	30	7	205.105637	191.151845	-94.303690	9.929504e-06
XEK.5	28	19	204.299162	179.912351	-71.824702	1.304541e-10		*
XEC.2.2	273	19	200.563447	180.563447	-73.126894	2.511427e-10		*
XEC.8	592	19	200.384129	185.805217	-83.610434	4.738311e-08		*
XEC.39	155	19	198.117564	178.117564	-68.235128	2.178063e-11		*
XEC.9	305	19	197.347986	171.265171	-54.530342	2.296052e-14		*
XEC.29	135	19	197.226078	168.663000	-49.326000	1.705360e-15		*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 515_520, 670_T|G, 829_C|T, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4181_G|T, 4184_G|A, 4321_C|T, 6183_A|G, 6250_C|T, 6402_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14184_C|T,
14408_C|T, 15714_C|T, 15756_T|A, 16338_C|T, 17410_C|T, 17856_A|G, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19028_A|G, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTNT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27579_27581, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29272_C|T, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ253899



Target: 5350 samples       Number of changes: 144                                                   
BC: XEC.6 + XEC.2          BC BR: 13-14                    BC BR coord: 4387 - 4388          
Direction L1: <<           Initial region span: 1-13,17-144 Gap history (edge excluded): 13-17
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 8.80e-33 Rec. model vs L2: 7.20e-25                                               
Flags: Model_2BP_Bad_L1_opp

XEC.6 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.6	45	13	26.742494	NaN	NaN	NaN	*	*	*
PG.3	31	13	26.401080	26.401080	-26.802160	0.711770	*	*
XEC.28	39	13	24.665462	24.665462	-23.330925	0.125556	*	*
XEC.4	192	15	23.051273	16.214163	-6.428326	0.000027	*
XEC.5	126	15	22.432474	16.154980	-6.309960	0.000025	*
MC.24	831	15	22.393442	18.004705	-10.009410	0.000161	*
KP.3.1	1957	15	21.637916	18.510306	-11.020613	0.000267	*
XEC.25	13	15	20.947831	13.497616	-0.995232	0.000002
XEC.32	42	15	19.732255	13.454761	-0.909521	0.000002
KP.3.1.1	12013	15	19.340654	16.323422	-6.646844	0.000030	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	17	266.291455	NaN	NaN	NaN	*	*	*
KP.3.3	1715	4	243.753457	226.915786	-167.831572	1.213825e-15
XEC.9	305	17	234.878537	212.405513	-138.811025	6.060983e-22		*
XEC.2.2	273	24	233.676393	211.916366	-137.832731	3.713118e-22
XEC.18	165	4	231.254683	209.821902	-133.643803	4.569744e-23
XEC.39	155	4	229.918031	208.500871	-131.001741	1.220740e-23
XEC.38	34	4	229.839194	208.460304	-130.920608	1.172874e-23
XEC.6	45	1	228.039001	201.296507	-116.593014	9.068415e-27
XEC.4	192	4	227.712175	206.301116	-126.602231	1.352618e-24
XEC.14	193	6	227.533320	207.192026	-128.384052	3.293801e-24

Target sequence

, 21_C|T, 44_C|T, 222_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6027_C|T, 6183_A|G, 6476_G|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 9679_C|T, 10029_C|T, 10198_C|T, 10369_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16323_C|T, 16362_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28651_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ253914



Target: 5350 samples       Number of changes: 142                                                   
BC: XEC.6 + XEC.2          BC BR: 12-13                    BC BR coord: 4387 - 4388          
Direction L1: <<           Initial region span: 1-10,16-142 Gap history (edge excluded): 10-16
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 8.13e-33 Rec. model vs L2: 6.85e-25                                               
Flags: Model_2BP_Bad_L1_opp

XEC.6 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.6	45	10	21.025611	NaN	NaN	NaN	*	*	*
PG.3	31	10	20.727304	19.281664	-12.563327	0.759572	*	*
XEC.28	39	10	18.857113	17.342480	-8.684961	0.109154	*	*
XEC.4	192	14	15.813411	8.976300	8.047400	0.000025	*
MC.24	831	14	15.151503	10.762766	4.474469	0.000152	*
XEC.5	126	14	15.141493	8.863999	8.272003	0.000023	*
KP.3.1	1957	14	14.414457	11.286848	3.426305	0.000256	*
XEC.25	13	14	13.624849	6.174634	13.650732	0.000002
XFB.3	56	6	13.391693	6.606966	12.786068	0.000002
KP.2.28.1	10	6	13.318834	6.459999	13.080002	0.000002

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	16	262.717046	NaN	NaN	NaN	*	*	*
XEC.2.2	273	22	233.526708	204.605241	-121.210482	3.244211e-22
XEC.9	305	22	232.585592	205.179474	-122.358947	5.765386e-22
KP.3.3	1715	4	229.224421	219.650556	-151.301113	1.109352e-15
XEC.15	127	25	225.043735	188.942343	-89.884685	5.103710e-29
XEC.18	165	22	224.090972	202.773748	-117.547495	5.204154e-23
XEC.39	155	22	222.729770	201.393521	-114.787043	1.309254e-23
XEC.14	193	22	221.334989	200.011685	-112.023371	3.277373e-24
XEC.38	34	16	221.162256	201.169104	-114.338208	1.045460e-23		*
XEC.2.1	265	25	220.942991	181.215578	-74.431156	2.254037e-32

Target sequence

, 21_C|T, 44_C|T, 222_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 6027_C|T, 6183_A|G, 6476_G|T, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 9679_C|T, 10029_C|T, 10198_C|T, 10369_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16323_C|T, 16362_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28651_C|T, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ253899



Target: 5350 samples       Number of changes: 144                                                   
BC: XEC.6 + XEC.2          BC BR: 13-14                    BC BR coord: 4387 - 4388          
Direction L1: <<           Initial region span: 1-13,17-144 Gap history (edge excluded): 13-17
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 8.80e-33 Rec. model vs L2: 7.20e-25                                               
Flags: Model_2BP_Bad_L1_opp

XEC.6 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.6	45	13	26.742494	NaN	NaN	NaN	*	*	*
PG.3	31	13	26.401080	26.401080	-26.802160	0.711770	*	*
XEC.28	39	13	24.665462	24.665462	-23.330925	0.125556	*	*
XEC.4	192	15	23.051273	16.214163	-6.428326	0.000027	*
XEC.5	126	15	22.432474	16.154980	-6.309960	0.000025	*
MC.24	831	15	22.393442	18.004705	-10.009410	0.000161	*
KP.3.1	1957	15	21.637916	18.510306	-11.020613	0.000267	*
XEC.25	13	15	20.947831	13.497616	-0.995232	0.000002
XEC.32	42	15	19.732255	13.454761	-0.909521	0.000002
KP.3.1.1	12013	15	19.340654	16.323422	-6.646844	0.000030	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	17	266.291455	NaN	NaN	NaN	*	*	*
KP.3.3	1715	4	243.753457	226.915786	-167.831572	1.213825e-15
XEC.9	305	17	234.878537	212.405513	-138.811025	6.060983e-22		*
XEC.2.2	273	24	233.676393	211.916366	-137.832731	3.713118e-22
XEC.18	165	4	231.254683	209.821902	-133.643803	4.569744e-23
XEC.39	155	4	229.918031	208.500871	-131.001741	1.220740e-23
XEC.38	34	4	229.839194	208.460304	-130.920608	1.172874e-23
XEC.6	45	1	228.039001	201.296507	-116.593014	9.068415e-27
XEC.4	192	4	227.712175	206.301116	-126.602231	1.352618e-24
XEC.14	193	6	227.533320	207.192026	-128.384052	3.293801e-24

Target sequence

 Case 72 (XEC): OZ253930



Target: 5350 samples       Number of changes: 143                                                   
BC: XEC.6 + XEC.2          BC BR: 12-13                    BC BR coord: 4387 - 4388          
Direction L1: <<           Initial region span: 1-10,16-143 Gap history (edge excluded): 10-16
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 8.29e-33 Rec. model vs L2: 6.85e-25                                               
Flags: Model_2BP_Bad_L1_opp

XEC.6 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.6	45	10	21.025611	NaN	NaN	NaN	*	*	*
PG.3	31	10	20.727304	19.281664	-12.563327	0.759572	*	*
XEC.28	39	10	18.857113	17.342480	-8.684961	0.109154	*	*
XEC.4	192	14	15.813411	8.976300	8.047400	0.000025	*
MC.24	831	14	15.151503	10.762766	4.474469	0.000152	*
XEC.5	126	14	15.141493	8.863999	8.272003	0.000023	*
KP.3.1	1957	14	14.414457	11.286848	3.426305	0.000256	*
XEC.25	13	14	13.624849	6.174634	13.650732	0.000002
XFB.3	56	6	13.391693	6.606966	12.786068	0.000002
KP.2.28.1	10	6	13.318834	6.459999	13.080002	0.000002

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	16	269.894683	NaN	NaN	NaN	*	*	*
XEC.2.2	273	22	240.701886	211.780418	-135.560837	3.244211e-22
XEC.9	305	22	239.769711	212.363593	-136.727186	5.823329e-22
KP.3.3	1715	4	236.412347	226.838482	-165.676965	1.126118e-15
XEC.15	127	25	232.241012	196.139620	-104.279240	5.232911e-29
XEC.18	165	22	231.276091	209.958867	-131.917733	5.256457e-23
XEC.39	155	22	229.914102	208.577853	-129.155707	1.322412e-23
XEC.14	193	22	228.532266	207.208963	-126.417925	3.360340e-24
XEC.38	34	16	228.359533	208.366381	-128.732762	1.066580e-23		*
XEC.2.1	265	25	228.117497	188.390085	-88.780169	2.254037e-32

Target sequence

, 21_C|T, 44_C|T, 222_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 6027_C|T, 6183_A|G, 6476_G|T, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 9679_C|T, 10029_C|T, 10198_C|T, 10369_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16323_C|T, 16362_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28651_C|T,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ255358



Target: 5350 samples      Number of changes: 135                                                   
BC: XEC.29 + KP.3.1.1     BC BR: 46-47                    BC BR coord: 20059 - 20060        
Direction L1: <<          Initial region span: 1-10,50-135 Gap history (edge excluded): 10-50
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 2.36e-06                                                            
Rec. model vs L1: 5.27e-03 Rec. model vs L2: 1.14e-53                                               
Flags: Model_1BP_Best

XEC.29 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.29	135	10	25.810025	NaN	NaN	NaN	*	*	*
JN.1	17255	36	25.121783	14.172950	79.654101	4.242574e-02	*
LB.1.3	778	36	21.308170	-13.504411	135.008821	4.039784e-14
JN.1.13.1	751	36	19.360688	-9.658035	127.316070	1.888950e-12
LB.1	1128	36	18.607672	-1.801574	111.603149	4.895252e-09
XEC.17	13	46	16.950408	16.950408	74.099183	6.804506e-01	*
KP.3.3	1715	36	16.606773	7.137632	93.724735	3.735664e-05	*
XEC.38	34	46	16.591667	16.591667	74.816666	4.747343e-01	*
KP.3.1	1957	34	16.565975	-6.886910	121.773821	3.029616e-11
XEC.5	126	46	16.560985	16.560985	74.878031	4.607038e-01	*

|||||

KP.3.1.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.1	12013	50	143.178104	NaN	NaN	NaN	*	*	*
XEC.17	13	50	134.965102	95.979602	18.040797	1.609109e-08		*
MR.2	14	50	134.332198	96.615330	16.769339	3.036425e-08		*
XEC.15	127	50	131.381088	89.512564	30.974873	2.505369e-11		*
XEC.2	921	40	131.309845	110.462585	-10.925169	3.142976e-02	*
XEK.1.2	33	50	131.302972	94.874388	20.251223	5.329545e-09		*
XEC.2.2	273	50	131.181543	97.722242	14.555517	9.167648e-08		*
XEC.9	305	50	131.139648	97.469838	15.060324	7.139771e-08		*
XEK.5	28	50	131.079532	97.365644	15.268712	6.428111e-08		*
XEC.25	13	50	131.070597	93.759877	22.480245	1.747639e-09		*

Target sequence

, 37_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3682_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7360_G|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10396_G|T, 10447_G|A, 10449_C|A, 11042_G|T, 11727_G|A, 12667_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16257_T|C, 17410_C|T, 18116_A|G, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20400_A|G, 21738_T|C, 21752_T|A, 21941_G|T, 21987_G|A, 22032_T|C, 22033_C|A,
22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T,
22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24460_T|C, 24469_T|A, 24872_G|T,
24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 26966_T|C, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28913_G|A, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ256652



Target: 5350 samples       Number of changes: 145                                                   
BC: XEC.6 + XEC.2          BC BR: 13-14                    BC BR coord: 4387 - 4388          
Direction L1: <<           Initial region span: 1-13,17-145 Gap history (edge excluded): 13-17
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 9.44e-33 Rec. model vs L2: 7.20e-25                                               
Flags: Model_2BP_Bad_L1_opp

XEC.6 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.6	45	13	26.742494	NaN	NaN	NaN	*	*	*
PG.3	31	13	26.401080	26.401080	-26.802160	0.711770	*	*
XEC.28	39	13	24.665462	24.665462	-23.330925	0.125556	*	*
XEC.4	192	15	23.051273	16.214163	-6.428326	0.000027	*
XEC.5	126	15	22.432474	16.154980	-6.309960	0.000025	*
MC.24	831	15	22.393442	18.004705	-10.009410	0.000161	*
KP.3.1	1957	15	21.637916	18.510306	-11.020613	0.000267	*
XEC.25	13	15	20.947831	13.497616	-0.995232	0.000002
XEC.32	42	15	19.732255	13.454761	-0.909521	0.000002
KP.3.1.1	12013	15	19.340654	16.323422	-6.646844	0.000030	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	17	273.484845	NaN	NaN	NaN	*	*	*
KP.3.3	1715	4	251.001493	234.163823	-182.327646	1.282455e-15
XEC.9	305	17	242.162397	219.689373	-153.378745	6.631772e-22		*
XEC.2.2	273	24	240.646500	218.886472	-151.772944	2.964985e-22
XEC.18	165	4	238.577416	217.144635	-148.289270	5.204154e-23
XEC.39	155	4	237.246168	215.829008	-145.658015	1.397182e-23
XEC.38	34	4	237.102221	215.723331	-145.446663	1.257917e-23
XEC.6	45	1	235.300594	208.558100	-131.116200	9.725949e-27
XEC.4	192	4	234.974530	213.563471	-141.126942	1.450694e-24
XEC.14	193	6	234.785285	214.443992	-142.887983	3.497478e-24

Target sequence

, 21_C|T, 44_C|T, 222_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6027_C|T, 6183_A|G, 6476_G|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 9679_C|T, 10029_C|T, 10198_C|T, 10369_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16323_C|T, 16362_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28651_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ259254



Target: 5350 samples       Number of changes: 145                                                   
BC: XEC.6 + XEC.2          BC BR: 12-13                    BC BR coord: 4387 - 4388          
Direction L1: <<           Initial region span: 1-10,16-145 Gap history (edge excluded): 10-16
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 8.85e-33 Rec. model vs L2: 6.85e-25                                               
Flags: Model_2BP_Bad_L1_opp

XEC.6 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.6	45	10	21.025611	NaN	NaN	NaN	*	*	*
PG.3	31	10	20.727304	19.281664	-12.563327	0.759572	*	*
XEC.28	39	10	18.857113	17.342480	-8.684961	0.109154	*	*
XEC.4	192	14	15.813411	8.976300	8.047400	0.000025	*
MC.24	831	14	15.151503	10.762766	4.474469	0.000152	*
XEC.5	126	14	15.141493	8.863999	8.272003	0.000023	*
KP.3.1	1957	14	14.414457	11.286848	3.426305	0.000256	*
XEC.25	13	14	13.624849	6.174634	13.650732	0.000002
XFB.3	56	6	13.391693	6.606966	12.786068	0.000002
KP.2.28.1	10	6	13.318834	6.459999	13.080002	0.000002

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	16	280.689930	NaN	NaN	NaN	*	*	*
KP.3.3	1715	4	250.866270	241.292405	-192.584810	1.183855e-15
XEC.9	305	16	249.326363	226.853339	-163.706678	6.371737e-22		*
XEC.2.2	273	23	247.671992	225.911965	-161.823929	2.476564e-22
XEC.18	165	16	240.865537	224.475328	-158.950656	5.897079e-23		*
XEC.39	155	16	239.508558	223.111877	-156.223753	1.506000e-23		*
XEC.38	34	16	239.225503	222.835294	-155.670589	1.143916e-23		*
XEC.15	127	26	239.170347	210.259030	-130.518061	3.954949e-29
XEC.14	193	16	238.057023	221.666814	-153.333628	3.550336e-24		*
XEC.29	135	26	235.472903	198.653095	-107.306190	3.607060e-34

Target sequence

, 21_C|T, 44_C|T, 222_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 6027_C|T, 6183_A|G, 6476_G|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 9679_C|T, 10029_C|T, 10198_C|T, 10369_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16323_C|T, 16362_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28651_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): OZ260197



Target: 5350 samples       Number of changes: 140                                                   
BC: XEC.39 + XEK.5         BC BR: 48-49                    BC BR coord: 21642 - 21643        
Direction L1: <<           Initial region span: 1-45,49-140 Gap history (edge excluded): 45-49
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 1.39e-16 Rec. model vs L2: 5.16e-60                                               
Flags: Model_2BP_Bad_L1_opp

XEC.39 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.39	155	45	38.388351	NaN	NaN	NaN	*	*	*
JN.1	17255	35	35.082955	8.702492	96.595016	2.368471e+03	*
LB.1.3	778	35	30.639802	-46.981661	207.963323	1.559378e-21
JN.1.13.1	751	35	30.478946	-27.966205	169.932410	2.825276e-13
LB.1	1128	35	27.504427	-24.832603	163.665205	6.462532e-12
KP.3.3	1715	35	26.542676	-9.338321	132.676642	3.465738e-05	*
XEC.16	23	45	26.473286	-22.433528	158.867056	7.123762e-11		*
XEC.17	13	45	26.473286	-22.573290	159.146580	6.193102e-11		*
XEC.24	11	45	26.473286	-22.573290	159.146580	6.193102e-11		*
XEC.32	42	45	26.449188	-9.721779	133.443557	2.370084e-05	*	*

|||||

XEK.5 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEK.5	28	49	167.609174	NaN	NaN	NaN	*	*	*
XEC.2	921	15	165.473003	153.682053	-113.364106	8.918214e-07
KP.3.3	1715	48	162.348195	159.657421	-125.314843	3.509033e-04	*	*
XEC.36	30	49	159.756236	159.756236	-125.512473	3.878081e-04	*	*
XEK.2	67	49	159.320949	159.320949	-124.641899	2.510145e-04	*	*
KP.3.1.1	12013	49	158.943749	154.275478	-114.550956	1.616900e-06		*
XEC.19	59	48	157.436406	153.609593	-113.219187	8.315287e-07		*
XEC.15	127	48	157.035680	153.975517	-113.951035	1.197829e-06		*
XEC.2.2	273	48	156.139292	153.844414	-113.688828	1.051808e-06		*
XEC.31	66	48	155.698571	153.775635	-113.551270	9.806992e-07		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1929_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3682_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7360_G|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10396_G|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16257_T|C,
17410_C|T, 18116_A|G, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20151_T|C, 20400_A|G, 21641_G|T, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22264_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T,
22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
26966_T|C, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28913_G|A, 28958_C|A,
29510_A|C, 29734_29759

 Case 72 (XEC): USA/2607442/2025



Target: 5350 samples       Number of changes: 143                                               
BC: BA.5.11 + XEC.18       BC BR: 5-6                    BC BR coord: 686 - 687          
Direction L1: <<           Initial region span: 1-4,9-143 Gap history (edge excluded): 4-9
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 5.03e-08                                           
Flags: Model_2BP_Bad_L1_opp

BA.5.11 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
BA.5.11	989	4	8.106025	NaN	NaN	NaN	*	*	*
HN.8	13	4	6.801549	-3.198451	18.396902	0.000013	*	*
DE.1	90	5	6.620049	6.620049	-1.240099	0.247833	*	*
BG.5	669	4	6.256906	5.277064	1.445873	0.064570	*	*
BA.4.6	19369	5	5.986448	5.986448	0.027103	0.131336	*	*
CM.2	356	4	5.668259	5.655743	0.688515	0.094420	*	*
BQ.1.12	2465	4	5.363047	4.647657	2.704685	0.034562	*	*
BA.5	6418	5	4.399094	4.399094	3.201813	0.026917	*	*
BA.5.2.2	625	4	4.194037	3.464549	5.070903	0.010567	*	*
BA.2.72	344	4	4.129940	2.205802	7.588396	0.002997	*	*

|||||

XEC.18 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.18	165	9	262.874907	NaN	NaN	NaN	*	*	*
XEC.14	193	13	260.502314	241.476221	-168.952441	6.604527e-03	*
XEC.19	59	19	260.246855	237.394599	-160.789198	1.116658e-04	*
KP.3.3	1715	13	259.567101	246.364005	-178.728010	8.780954e-01	*
XEC.2	921	19	258.077153	227.506625	-141.013250	5.659105e-09
XEC.33	169	13	250.232992	231.197954	-148.395908	2.277539e-07
XEC.2.2.1	46	19	249.832308	201.401210	-88.802420	2.603097e-20
XEK.1.2	33	19	249.196523	179.530173	-45.060346	8.269324e-30
XEC.2.1	265	19	248.840825	208.650527	-103.301054	3.665433e-17
XEC.29	135	19	247.254376	217.222809	-120.445619	1.941782e-13

Target sequence

, 241_C|T, 388_G|A, 509_523, 670_T|G, 686_694, 884_C|T, 897_C|A, 1780_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3213_A|G, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6198_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23285_G|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27476_C|T, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/AL-CDC-LC1136375/2025



Target: 5350 samples       Number of changes: 147                                                 
BC: ML.2 + XEC.8           BC BR: 4-5                     BC BR coord: 896 - 897           
Direction L1: <<           Initial region span: 1-4,17-147 Gap history (edge excluded): 4-17
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  -                                                                             
Rec. model vs L1: 1.94e-89 Rec. model vs L2: 1.36e-07                                             
Flags: Model_2BP_Bad_L1_opp

ML.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
ML.2	67	4	10.429993	NaN	NaN	NaN	*	*	*
XEC.5	126	7	7.088026	-5.313181	18.626363	1.452223e-07
KP.1.1.3	979	4	6.752912	6.752912	-5.505824	2.534941e-02	*	*
LB.1	1128	4	6.623602	6.623602	-5.247205	2.225920e-02	*	*
KP.2.3	4440	4	5.262138	5.262138	-2.524276	5.684569e-03	*	*
BQ.1.1.13	384	3	5.209197	-4.790803	17.581606	2.454924e-07		*
BN.1	1200	3	4.758002	-5.241998	18.483997	1.565328e-07		*
BA.5.2.25	225	3	4.643280	-5.356720	18.713440	1.395281e-07		*
BA.2.6	424	3	4.011740	-5.988260	19.976520	7.394088e-08		*
JN.1	17255	4	3.898572	3.898572	0.202856	1.459006e-03	*	*

|||||

XEC.8 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.8	592	17	239.838590	NaN	NaN	NaN	*	*	*
XEC.2	921	17	235.955115	192.152673	-72.305346	6.983891e-13		*
XEC.31	66	17	233.874147	206.296200	-100.592401	9.660985e-07		*
XEC.13	30	9	230.779072	218.142681	-124.285362	1.353353e-01	*
XEC.4	192	17	226.152775	206.470555	-100.941109	1.150861e-06		*
XEC.9	305	17	225.877310	200.107992	-88.215984	1.990261e-09		*
XEC.5	126	3	225.426010	220.743758	-129.487515	1.822119e+00	*
KP.3.3	1715	17	224.619573	196.008512	-80.017024	3.298395e-11		*
XEC.16	23	17	222.913957	203.274296	-94.548592	4.714679e-08		*
XEC.15	127	32	218.705506	196.333501	-80.667001	4.565080e-11

Target sequence

, 241_C|T, 548_A|G, 670_T|G, 897_C|A, 1221_C|T, 2060_G|A, 2790_C|T, 2883_G|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5184_C|A, 6183_A|G, 6504_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11647_T|C, 11727_G|A, 12119_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18490_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21595_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21759_A|G, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T,
25584_C|T, 25947_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/AZ-CDC-LC1136724/2025



Target: 5350 samples          Number of changes: 146                                                                  
BC: XEC.2.1 + JN.1.4 + XEC.2.1 BC BR: 10-11, 29-30                   BC BR coord: 4330 - 4331, 11726 - 11727    
Direction L1: <<              Initial region span: 1-10,14-29,30-146 Gap history (edge excluded): 10-30 -> 10-14
Alt. candidates: [], []                                                                                                      
Model 1BP/2BP comparison:     2BP vs 1BP: 7.79e-01                                                                           
Rec. model vs L1: 1.51e-27    Rec. model vs L2: 1.02e-67                                                              
Flags: Model_2BP_Best

XEC.2.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2.1	265	10	5.110242	None	None	None	*	*	*

|||||

JN.1.4 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.4	8971	14	21.326646	NaN	NaN	NaN	*	*	*
KP.3.1.1	12013	16	18.403504	0.446263	45.107473	1.122064e-02	*
JN.1	17255	16	17.393277	12.515814	20.968372	1.958629e+03	*
NL.19	18	16	13.363880	-9.423386	64.846772	5.801379e-07
JN.1.59	77	16	11.203885	-11.583381	69.166762	6.690447e-08
JN.1.16.1	466	16	10.959804	-11.833912	69.667823	5.210526e-08
NW.1	111	16	10.806076	-14.194619	74.389238	4.919790e-09
MC.42	84	16	10.676479	-16.497598	78.995197	4.907923e-10
BA.5.2.58	299	28	8.808574	-81.665569	209.331138	2.455262e-38
MC.19	221	16	8.767825	-18.406252	82.812504	7.304101e-11

|||||

XEC.2.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2.1	265	30	239.456143	NaN	NaN	NaN	*	*	*
XEC.21	38	30	234.529655	255.972354	-251.944707	8.976945e+04	*	*
XEC.29	135	30	228.715062	250.162069	-240.324138	2.690777e+02	*	*
XEC.13	30	30	225.221545	246.657011	-233.314021	8.084915e+00	*	*
XEC.39	155	1	220.009808	233.192331	-206.384661	1.147890e-05	*
XEC.31	66	30	218.854723	240.278288	-220.556576	1.377362e-02	*	*
XEK.1	88	30	218.726667	223.898205	-187.796410	1.059997e-09		*
XEC.25	13	30	218.450885	239.920252	-219.840505	9.609530e-03	*	*
XEK.5	28	30	218.334071	223.442929	-186.885858	6.725128e-10		*
XEC.33	169	30	218.310880	239.708276	-219.416552	7.789333e-03	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5833_C|T, 6183_A|G, 7216_T|C, 7842_A|G, 8248_T|A, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10738_T|C, 11042_G|T, 11083_G|T, 11288_11296, 11479_C|T, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18123_T|C, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26497_T|G, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28697_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/CA-CDC-2-8448546/2025



Target: 5350 samples         Number of changes: 144                                                             
BC: KP.3.3 + MC.33.1 + KP.3.3 BC BR: 5-6, 9-10                   BC BR coord: 2792 - 2793, 3566 - 3567    
Direction L1: <<             Initial region span: 1-5,6-9,13-144 Gap history (edge excluded): 5-13 -> 9-13
Alt. candidates: [], []                                                                                                
Model 1BP/2BP comparison:    2BP vs 1BP: 3.31e-01                                                                      
Rec. model vs L1: 2.31e-07   Rec. model vs L2: 1.23e-156                                                        
Flags: Model_2BP_Best

KP.3.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.3	1715	5	7.484405	None	None	None	*	*	*

|||||

MC.33.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.33.1	85	9	12.609551	NaN	NaN	NaN	*	*	*
KP.2.3.4	70	9	12.110560	12.110560	-16.221119	6.065307e-01	*	*
KP.1.1	593	10	11.022576	9.944861	-11.889723	6.959935e-02	*	*
XFG.3	480	9	10.103287	10.103287	-12.206575	8.167560e-02	*	*
KP.3.1	1957	9	9.826179	9.826179	-11.652359	6.172909e-02	*	*
JN.1.4	8971	9	7.237165	7.237165	-6.474330	4.630919e-03	*	*
B.1.177.19	495	7	6.529220	-13.470780	34.941560	4.716284e-12
BF.14	1581	7	5.445294	-14.554706	37.109413	1.593641e-12
BA.2.9.7	243	7	4.728411	-15.271589	38.543179	7.795964e-13
BA.2.10.1	1369	7	4.540081	-15.459919	38.919837	6.446944e-13

|||||

KP.3.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.3	1715	13	252.932900	NaN	NaN	NaN	*	*	*
XEC.29	135	17	247.716863	211.551605	-119.103211	1.145706e-12
XEC.9	305	17	246.285430	218.002066	-132.004131	7.248909e-10
XEC.39	155	17	240.996777	218.809964	-133.619929	1.629488e-09
XEC.33	169	17	240.624092	229.368474	-154.736948	6.283489e-05	*
XEC.2	921	15	239.898054	210.334928	-116.669856	3.399425e-13
XEC.31	66	17	236.188008	206.073532	-108.147065	4.800770e-15
XEC.28	39	17	235.722025	218.895366	-133.790733	1.774051e-09
XEC.19	59	17	235.468024	206.467151	-108.934303	7.090646e-15
XEC.14	193	17	235.329662	213.142601	-122.285203	5.646417e-12

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3013_G|A, 3037_C|T, 3431_G|T, 3565_T|C, 3737_C|T, 3809_C|A, 4084_C|T, 4184_G|A, 4321_C|T, 6183_A|G, 6659_A|G, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 14655_T|C, 15156_T|C,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22343_G|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23929_C|T, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C

 Case 72 (XEC): USA/CA-CDPH-500146638/2025



Target: 5350 samples       Number of changes: 143                                                 
BC: XEC.38 + XEC.2         BC BR: 11-12                   BC BR coord: 4387 - 4388         
Direction L1: <<           Initial region span: 1-8,12-143 Gap history (edge excluded): 8-12
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  -                                                                             
Rec. model vs L1: 3.81e-28 Rec. model vs L2: 4.46e-19                                             
Flags: Model_2BP_Bad_L1_opp

XEC.38 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.38	34	8	13.172332	NaN	NaN	NaN	*	*	*
XEC.18	165	8	12.757409	4.904267	14.191466	0.660340	*	*
XEC.5	126	8	11.936888	4.067746	15.864509	0.286505	*	*
XEC.15	127	8	11.878843	4.025701	15.948597	0.273898	*	*
XEC.9	305	8	11.022016	3.165590	17.668819	0.115903	*	*
KP.3.3	1715	8	5.863847	-1.991046	27.982092	0.000669	*	*
XEC.4.6	10	8	5.589794	-2.263348	28.526696	0.000508	*	*
KP.3.1.1	12013	11	4.534174	4.534174	14.931653	0.456120	*
MC.24	831	8	3.990510	-3.865041	31.730083	0.000103	*	*
KP.3.1	1957	8	3.885854	-3.970870	31.941740	0.000092	*	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	12	238.277608	NaN	NaN	NaN	*	*	*
XEC.9	305	14	235.176910	222.703885	-155.407771	1.721327e-07
XEC.30	135	4	231.287337	224.635859	-159.271719	1.185910e-06
XEC.14	193	13	230.573028	220.573028	-151.146056	2.045579e-08		*
XEC.29	135	14	229.463795	209.076686	-128.153373	2.072190e-13
XEC.18	165	13	223.116326	213.116326	-136.232651	1.177550e-11		*
XEK.2	67	14	220.045290	200.719999	-111.439997	4.874154e-17
XEC.31	66	13	219.797799	209.797799	-129.595599	4.278516e-13		*
XEC.28	39	13	219.331816	202.357276	-114.714552	2.500177e-16		*
XEC.19	59	13	219.077815	202.290051	-114.580102	2.342834e-16		*

Target sequence

, 241_C|T, 670_T|G, 1191_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3754_A|G, 4184_G|A, 4321_C|T, 4890_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
9693_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18012_T|A,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24208_C|A, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25429_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29530_C|T

 Case 72 (XEC): USA/CA-CDPH-500146752/2025



Target: 5350 samples        Number of changes: 139                                                          
BC: XEC.14 + GW.5.2 + XEC.14 BC BR: 5-6, 8-9                   BC BR coord: 2792 - 2793, 3430 - 3431  
Direction L1: <<            Initial region span: 1-5,7-8,9-139 Gap history (edge excluded): 5-9 -> 5-7
Alt. candidates: [], []                                                                                            
Model 1BP/2BP comparison:   2BP vs 1BP: 7.97e-04                                                                   
Rec. model vs L1: 7.27e-09  Rec. model vs L2: 0.00e+00                                                      
Flags: Model_2BP_Best

XEC.14 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.14	193	5	4.213472	None	None	None	*	*	*

|||||

GW.5.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
GW.5.2	13	7	8.004421	NaN	NaN	NaN	*	*	*
NL.2	237	7	6.876263	-3.123737	12.247475	0.323033	*	*
NL.19	18	7	6.069561	-3.930439	13.860878	0.144424	*	*
BF.7.4.2	154	7	5.714739	-4.285261	14.570521	0.101266	*	*
JN.1.1.2	17	7	5.433572	-4.566428	15.132856	0.076536	*	*
B.1.293	36	7	5.376414	-4.623586	15.247173	0.072078	*	*
JN.1.7.3	19	7	5.322346	-4.677654	15.355307	0.068221	*	*
BN.1.2.6	25	7	5.047910	-4.952090	15.904181	0.052079	*	*
B.1.439	85	7	4.922746	-5.077254	16.154507	0.045959	*	*
HZ.3	65	7	4.785545	-5.214455	16.428909	0.039955	*	*

|||||

XEC.14 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.14	193	9	268.306840	NaN	NaN	NaN	*	*	*
XEC.17	13	9	267.094491	279.176919	-266.353838	776.657923	*	*
MC.24.1	25	9	264.690577	276.078257	-260.156514	35.163197	*	*
XEC.32	42	9	263.851395	275.933823	-259.867646	30.416949	*	*
XEC.4	192	9	263.429305	275.495985	-258.991969	19.589623	*	*
XEC.13	30	9	263.168841	275.251269	-258.502539	15.332887	*	*
XEC.38	34	9	263.150639	275.203214	-258.406429	14.658201	*	*
XEC.18	165	9	262.930734	274.994925	-257.989849	11.881707	*	*
XEC.24	11	9	262.864692	274.947120	-257.894240	11.302229	*	*
XEC.40	52	9	262.844209	274.887801	-257.775602	10.697392	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 2950_T|C, 3037_C|T, 3157_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12937_A|G, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G,
18483_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T,
26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28958_C|A, 29510_A|C

 Case 72 (XEC): USA/CA-CDPH-500146814/2025



Target: 5350 samples       Number of changes: 146                                                       
BC: XEC.8 + ML.1           BC BR: 138-139                    BC BR coord: 28361 - 28362          
Direction L1: >>           Initial region span: 1-138,140-146 Gap history (edge excluded): 138-140
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 7.03e-08 Rec. model vs L2: 8.68e-105                                                  
Flags: Model_2BP_Bad_L1_opp

XEC.8 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.8	592	138	238.071288	NaN	NaN	NaN	*	*	*
XEC.18	165	138	229.630397	229.630397	-159.260795	2.160502e-04	*	*
XEC.2	921	138	207.791442	207.791442	-115.582884	7.072339e-14		*
XEC.39	155	138	207.345136	207.345136	-114.690272	4.532127e-14		*
KP.3.3	1715	146	206.689729	192.967116	-85.934231	2.577196e-20
XEC.40	52	138	202.553265	202.553265	-105.106530	3.767311e-16		*
MC.24.1	25	138	198.183060	198.183060	-96.366120	4.766116e-18		*
XEC.5	126	138	195.644128	195.644128	-91.288256	3.758864e-19		*
XEC.9	305	138	194.894561	194.894561	-89.789121	1.775562e-19		*
XEC.30	135	138	194.239998	194.239998	-88.479996	9.223014e-20		*

|||||

ML.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
ML.1	13	140	13.599755	NaN	NaN	NaN	*	*	*
KP.3.3	1715	139	12.580304	12.580304	-1.160607	7.942632e+03	*	*
KP.3.3.4	292	140	10.380879	0.380879	23.238242	3.995506e-02	*	*
MC.25	26	144	7.903615	-18.702477	61.404955	2.066489e-10
MC.8.1	174	140	7.444087	-8.615746	41.231492	4.955562e-06		*
KP.4.1	198	140	7.294941	-2.705059	29.410119	1.827146e-03	*	*
LF.7.9.1	48	144	7.068786	-11.276717	46.553434	3.466327e-07
KR.1	62	144	6.968144	-18.073991	60.147982	3.860709e-10
MC.13.2	74	144	6.777607	-11.567896	47.135792	2.580790e-07
MC.21	25	144	6.597363	-11.748140	47.496280	2.155657e-07

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3896_G|A, 4184_G|A, 4321_C|T, 6183_A|G, 6226_T|C, 7842_A|G, 8293_C|T, 8393_G|A, 8869_T|C, 9344_C|T, 9424_A|G,
9534_C|T, 9565_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18105_G|T, 18163_A|G, 18294_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21766_A|T, 21767_21772, 21941_G|T, 21987_G|A, 21992_21994, 22000_C|T, 22009_C|T, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G,
22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A,
23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28618_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29171_C|T, 29510_A|C

 Case 72 (XEC): USA/CA-CDPH-500146886/2025



Target: 5350 samples      Number of changes: 144                                                               
BC: XEC.8 + LC.1 + XEC.8  BC BR: 8-9, 11-12                   BC BR coord: 3566 - 3567, 4330 - 4331     
Direction L1: <<          Initial region span: 1-8,9-11,14-144 Gap history (edge excluded): 8-14 -> 11-14
Alt. candidates: [], []                                                                                               
Model 1BP/2BP comparison: 2BP vs 1BP: 6.41e-01                                                                        
Rec. model vs L1: 1.86e-08 Rec. model vs L2: 7.77e-122                                                          
Flags: Model_2BP_Best

XEC.8 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.8	592	8	19.202242	None	None	None	*	*	*

|||||

LC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LC.1	10	11	10.630590	NaN	NaN	NaN	*	*	*
BA.5.1.36	33	11	9.947494	9.947494	-11.894987	0.504090	*	*
NY.7	36	11	9.637339	9.637339	-11.274677	0.369723	*	*
JN.1.1.3	30	11	9.126513	9.126513	-10.253026	0.222017	*	*
KP.4.1	198	11	8.332992	8.332992	-8.665985	0.100761	*	*
KL.1	39	11	8.171002	8.171002	-8.342003	0.085435	*	*
XBB.1.5.25	43	11	7.838524	7.838524	-7.677047	0.061421	*	*
XBB.2.3.2	378	10	7.121335	1.952073	4.095854	0.000170	*	*
XBB.1.16.14	142	11	6.878736	6.878736	-5.757472	0.023518	*	*
BE.1.3	218	11	6.440873	6.440873	-4.881746	0.015146	*	*

|||||

XEC.8 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.8	592	14	230.814875	NaN	NaN	NaN	*	*	*
XEC.2	921	14	224.156876	208.875386	-115.750773	6.591961e-10		*
XEC.2.2	273	14	218.046162	193.118221	-84.236442	9.477747e-17		*
KP.3.3	1715	15	211.959277	205.883036	-109.766072	3.314928e-11		*
XEC.32	42	14	211.675701	210.998210	-119.996420	5.519382e-09		*
XEC.4	192	14	209.961763	209.225965	-116.451929	9.354438e-10		*
XEC.31	66	14	202.380560	201.657267	-101.314535	4.824013e-13		*
XEC.28	39	14	201.989329	194.232704	-86.465408	2.890303e-16		*
XEC.14	193	14	201.687488	200.968193	-99.936386	2.431738e-13		*
XEC.19	59	14	201.664230	194.146789	-86.293579	2.641538e-16		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3949_T|C, 4184_G|A, 4321_C|T, 5365_C|T, 5800_G|A, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10460_A|G, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18739_G|A, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22116_A|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23608_G|T, 23854_C|A, 23948_G|T, 24376_T|C, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26822_C|T, 26833_C|T, 26858_C|T, 27134_T|C, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C

 Case 72 (XEC): USA/CA-CDPH-500146959/2025



Target: 5350 samples       Number of changes: 139                                                 
BC: XEC.4.3 + XEC.28       BC BR: 12-13                   BC BR coord: 5304 - 5305         
Direction L1: <<           Initial region span: 1-5,13-139 Gap history (edge excluded): 5-13
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  -                                                                             
Rec. model vs L1: 3.81e-42 Rec. model vs L2: 3.85e-17                                             
Flags: Model_2BP_Bad_L1_opp

XEC.4.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4.3	10	5	10.690412	NaN	NaN	NaN	*	*	*
XEC.12	71	5	7.632120	-3.009515	54.019029	4.573003e-02	*	*
XEC.18	165	5	7.475508	-3.155902	54.311804	3.955750e-02	*	*
KP.3.1.1	12013	12	5.510809	5.510809	36.978383	2.292928e+02	*
GJ.1.1	34	3	4.903037	-48.153258	144.306517	1.132341e-21
BA.2.9.5	117	3	4.738576	-52.375476	152.750953	1.664387e-23
BN.1.2.4	31	3	4.724144	-62.625128	173.250255	5.884858e-28
BA.5.5	23560	5	4.497932	-11.484322	70.968644	9.540163e-06		*
XEC.29	135	9	4.381687	-3.478890	54.957779	2.858137e-02	*
BQ.1.1.61	45	3	4.328996	-49.500977	147.001953	2.950197e-22

|||||

XEC.28 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.28	39	13	271.616993	NaN	NaN	NaN	*	*	*
XEC.2	921	7	271.327088	268.742601	-271.485203	5.669893e-02	*
XEC.14	193	4	267.240268	258.939453	-251.878906	3.128365e-06
XEC.39	155	7	264.205192	252.702429	-239.404858	6.099860e-09
XEC.31	66	11	261.944657	259.797799	-253.595599	7.392830e-06
XEC.9	305	4	260.403643	253.284773	-240.569546	1.094919e-08
XEC.17	13	11	259.858296	257.711438	-249.422875	9.143979e-07
XEC.19	59	13	259.077815	259.077815	-252.155630	3.598476e-06		*
MC.24.1	25	11	257.454382	255.307524	-244.615049	8.295231e-08
XEC.15	127	11	256.939211	254.792353	-243.584705	4.931685e-08

Target sequence

, 241_C|T, 670_T|G, 1150_C|T, 2060_G|A, 2790_C|T, 2902_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3768_C|T, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10156_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14346_G|A, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T,
26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28958_C|A, 29510_A|C

 Case 72 (XEC): USA/CA-CDPH-500146960/2025



Target: 5350 samples       Number of changes: 139                                           
BC: XEC.4.3 + XEC.14       BC BR: 4-5                    BC BR coord: 1153 - 1154    
Direction L1: <<           Initial region span: 1-4,5-139 Gap history (edge excluded):
Alt. candidates: [], []                                                                            
Model 1BP/2BP comparison:  -                                                                       
Rec. model vs L1: 1.08e-27 Rec. model vs L2: 3.85e-17                                       
Flags: Model_2BP_Bad_L1_opp

XEC.4.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4.3	10	4	10.581513	NaN	NaN	NaN	*	*	*
KP.3.3.10	55	4	9.569912	9.569912	-11.139824	0.364219	*	*
JN.1.34	83	4	8.927300	8.927300	-9.854600	0.191092	*	*
KS.2	18	4	8.837955	8.837955	-9.675911	0.175520	*	*
MC.10	221	4	8.648716	8.648716	-9.297431	0.145148	*	*
KP.2.3.13	25	4	8.566610	8.566610	-9.133220	0.133320	*	*
JN.1.40	26	4	8.488168	8.488168	-8.976337	0.123687	*	*
LZ.1	28	4	8.453281	8.453281	-8.906562	0.119433	*	*
NY.7	36	4	8.201967	8.201967	-8.403933	0.092551	*	*
JN.1.48.1	53	4	7.776727	7.776727	-7.553455	0.060507	*	*

|||||

XEC.14 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.14	193	5	277.240268	NaN	NaN	NaN	*	*	*
XEC.28	39	8	274.029392	271.367026	-250.734052	2.808794e-03	*
XEC.9	305	5	270.403643	270.403643	-248.807286	1.075467e-03	*	*
XEC.2	921	8	270.267362	251.343484	-210.686967	5.674719e-12
XEC.18	165	1	267.652679	260.292150	-228.584300	4.352197e-08
XEC.17	13	8	267.098377	264.461986	-236.923971	2.816544e-06
MC.24.1	25	8	264.694464	261.404146	-230.808292	1.327232e-07
XEC.29	135	5	264.350938	264.350938	-236.701875	2.523156e-06		*
XEC.15	127	8	264.097279	261.460888	-230.921775	1.402275e-07
XEC.32	42	8	263.855281	261.218890	-230.437780	1.103068e-07

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1150_C|T, 2060_G|A, 2790_C|T, 2902_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10156_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14346_G|A, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T,
26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28958_C|A, 29510_A|C

 Case 72 (XEC): USA/CA-CDPH-500146970/2025



Target: 5350 samples       Number of changes: 143                                                       
BC: XEC.4 + MC.11          BC BR: 140-141                    BC BR coord: 28883 - 28884          
Direction L1: >>           Initial region span: 1-135,141-143 Gap history (edge excluded): 135-141
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 2.26e-06 Rec. model vs L2: 8.78e-121                                                  
Flags: Model_2BP_Bad_L1_opp

XEC.4 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4	192	135	272.368594	NaN	NaN	NaN	*	*	*
XEC.9	305	135	245.645723	241.867956	-183.735912	2.549816e-12		*
XEC.39	155	135	245.430082	241.639328	-183.278655	2.025914e-12		*
XEC.12	71	135	244.154187	240.376420	-180.752840	5.717926e-13		*
KP.3.3	1715	141	240.977300	237.369000	-174.737999	2.832589e-14
MC.24.1	25	135	240.527506	236.095813	-172.191626	7.915132e-15		*
XEC.32	42	135	236.999882	233.222115	-166.444230	4.465412e-16		*
XEC.8	592	135	232.153215	228.375448	-156.750895	3.513215e-18		*
XEC.24	11	135	231.567155	221.586271	-143.172541	3.952258e-21		*
XEC.18	165	135	231.024563	221.565082	-143.130165	3.873998e-21		*

|||||

MC.11 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.11	393	141	6.592898	NaN	NaN	NaN	*	*	*
KP.3.1	1957	137	5.468303	5.040140	-2.080280	0.211189	*
KP.3.1.1	12013	141	3.166689	3.166689	1.666621	0.032387	*	*
JN.1	17255	141	2.880376	2.880376	2.239248	0.024355	*	*
KP.3.3.1	211	136	0.527997	-6.481903	20.963806	0.000002

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2054_G|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6322_T|C, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G,
18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20157_T|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25039_T|C, 25207_C|T, 25521_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28531_C|T, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29468_G|C, 29510_A|C

 Case 72 (XEC): USA/CA-CDPH-500146971/2025



Target: 5350 samples            Number of changes: 143                                                      
BC: XEC.32 + XBB.1.5.32 + XEC.32 BC BR: 3-4, 6-7                   BC BR coord: 896 - 897, 1539 - 1540
Direction L1: <<                Initial region span: 1-3,4-6,7-143 Gap history (edge excluded): 3-7 ->
Alt. candidates: [], []                                                                                            
Model 1BP/2BP comparison:       2BP vs 1BP: 8.70e-07                                                               
Rec. model vs L1: 1.29e-20      Rec. model vs L2: 0.00e+00                                                  
Flags: Model_2BP_Best

XEC.32 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.32	42	3	4.718819	None	None	None	*	*	*

|||||

XBB.1.5.32 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XBB.1.5.32	734	6	10.203883	NaN	NaN	NaN	*	*	*
GC.2	35	4	7.204670	-12.795330	31.590660	1.026188e-10
BA.2.9.1	448	4	7.204670	-12.795330	31.590660	1.026188e-10
GC.1	14	4	7.204670	-12.795330	31.590660	1.026188e-10
XBB.1.5.21	611	4	7.204670	-12.795330	31.590660	1.026188e-10
XBB.2.3	695	6	5.855443	5.855443	-5.710885	1.290681e-02	*	*
XBB.1.5.76	79	5	5.807614	-4.192386	14.384772	5.601843e-07		*
BQ.1.1.68	694	6	5.572080	5.572080	-5.144161	9.706107e-03	*	*
LY.1	178	5	5.281555	-4.718445	15.436890	3.297273e-07		*
BA.5.2.54	62	4	5.023446	-14.976554	35.953108	1.160019e-11

|||||

XEC.32 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.32	42	7	256.092276	NaN	NaN	NaN	*	*	*
XEC.15	127	7	253.778424	258.481370	-214.962740	9.729575e-02	*	*
XEC.2	921	8	252.085212	246.766770	-191.533540	7.949394e-07		*
XEC.28	39	7	251.832118	256.472318	-210.944637	1.303653e-02	*	*
XEC.9	305	7	251.375146	256.057623	-210.115245	8.651695e-03	*	*
XEC.8	592	7	249.630700	254.280707	-206.561414	1.459006e-03	*	*
XEC.14	193	7	245.674335	250.367016	-198.734033	2.909338e-05	*	*
XEC.17	13	7	244.461986	249.180805	-196.361610	8.895189e-06		*
XEC.29	135	7	243.813481	248.532300	-195.064600	4.643696e-06		*
MC.24.1	25	7	241.404146	246.082143	-190.164287	4.007212e-07		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1230_A|G, 1302_C|T, 1537_T|C, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14403_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19255_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23464_T|C,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28498_C|T,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29708_C|T

 Case 72 (XEC): USA/CA-CDPH-500146973/2025



Target: 5350 samples       Number of changes: 140                                           
BC: XBB.2.3.11 + XEC.32    BC BR: 4-5                    BC BR coord: 1539 - 1540    
Direction L1: <<           Initial region span: 1-4,5-140 Gap history (edge excluded):
Alt. candidates: [], []                                                                            
Model 1BP/2BP comparison:  -                                                                       
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 1.40e-14                                       
Flags: Model_2BP_Bad_L1_opp

XBB.2.3.11 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XBB.2.3.11	240	4	6.996488	NaN	NaN	NaN	*	*	*
DY.1	151	3	6.634900	-3.365100	16.730200	0.000032	*	*
BQ.1.1.68	694	4	5.994129	5.994129	-1.988257	0.367879	*	*
BA.2.9.4	37	3	5.920999	-4.079001	18.158003	0.000015	*	*
BF.7.4.2	154	3	5.181596	-4.818404	19.636807	0.000007		*
EY.1	81	3	4.707001	-5.292999	20.585998	0.000005		*
BA.5.2.18	582	3	4.359080	-5.640920	21.281840	0.000003		*
BA.2.3.13	70	3	4.184809	-5.815191	21.630382	0.000003		*
XBB.1.5.32	734	4	4.143742	4.143742	1.712516	0.057844	*	*
CH.1.1.15	87	3	3.967396	-6.032604	22.065208	0.000002		*

|||||

XEC.32 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.32	42	5	266.092276	NaN	NaN	NaN	*	*	*
XEC.15	127	5	263.778424	263.778424	-233.556848	9.926125e-02	*	*
XEC.2	921	6	262.085212	252.085212	-210.170424	8.273815e-07		*
XEC.28	39	5	261.832118	261.832118	-229.664237	1.412230e-02	*	*
XEC.9	305	5	261.375146	261.375146	-228.750292	8.959866e-03	*	*
XEC.8	592	5	259.630700	259.630700	-225.261399	1.564796e-03	*	*
XEC.14	193	5	255.674335	255.674335	-217.348670	2.997940e-05	*	*
XEC.17	13	5	254.461986	254.461986	-214.923971	8.895189e-06		*
XEC.29	135	5	253.813481	253.813481	-213.626962	4.666972e-06		*
MC.24.1	25	5	251.404146	251.404146	-208.808292	4.191655e-07		*

Target sequence

, 241_C|T, 670_T|G, 1302_C|T, 1537_T|C, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T,
18894_C|T, 19255_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23464_T|C, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28498_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28958_C|A, 29510_A|C, 29708_C|T

 Case 72 (XEC): USA/CA-CDPH-500147141/2025



Target: 5350 samples       Number of changes: 145                                                 
BC: BF.7.14.4 + XEC.2      BC BR: 3-4                     BC BR coord: 1086 - 1087         
Direction L1: <<           Initial region span: 1-3,15-145 Gap history (edge excluded): 3-15
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  -                                                                             
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 1.15e-17                                             
Flags: Model_2BP_Bad_L1_opp

BF.7.14.4 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
BF.7.14.4	36	3	8.723240	NaN	NaN	NaN	*	*	*
BF.7.14.1	39	3	8.723240	8.723240	-9.446479	1.000000	*	*
BF.7.14	256	3	8.699648	8.699648	-9.399296	0.975310	*	*
BF.7.14.5	65	3	8.691987	8.691987	-9.383974	0.965605	*	*
BF.7.14.6	77	3	7.688789	7.688789	-7.377579	0.355226	*	*
BQ.1.1.1	1179	4	6.377713	4.041056	-0.082112	0.009233	*	*
BF.7.26	89	4	6.148014	4.223304	-0.446607	0.011109	*	*
BA.2.75.1	232	3	5.906902	5.906902	-3.813803	0.059606	*	*
BA.5.2.49	19	3	5.778801	5.778801	-3.557601	0.052602	*	*
BQ.1.32	36	3	5.139721	5.139721	-2.279441	0.027737	*	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	15	256.201769	NaN	NaN	NaN	*	*	*
XEC.18	165	8	240.910533	217.190855	-112.381709	6.175010e-06
XEC.19	59	29	225.880841	184.868632	-47.737264	5.678584e-20
XEK.1.2	33	29	225.131652	130.854745	60.290511	1.976167e-43
XEC.33	169	29	224.551586	194.553372	-67.106744	9.128136e-16
XEC.2.1	265	29	224.339400	165.353465	-8.706929	1.901005e-28
XEC.14	193	29	223.332651	189.092540	-56.185081	3.882703e-18
KP.3.3	1715	8	223.213774	214.490035	-106.980070	4.149947e-07
XEC.2.2.1	46	29	222.329755	148.013289	25.973423	5.601662e-36
XEC.29	135	26	216.040490	175.948870	-29.897740	7.591599e-24

Target sequence

, 241_C|T, 670_T|G, 1085_G|T, 1387_C|T, 1471_C|T, 2060_G|A, 2395_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4754_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 9693_C|T, 10029_C|T, 10198_C|T, 10199_A|T, 10447_G|A, 10449_C|A, 10702_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25668_A|G, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27476_C|T, 27604_G|A, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29499_A|T, 29510_A|C

 Case 72 (XEC): USA/CA-LACPHL-AY11141/2025



Target: 5350 samples       Number of changes: 147                                                          
BC: XEC.2 + XEC.4.1 + XEC.2 BC BR: 4-5, 7-8                   BC BR coord: 941 - 942, 2789 - 2790    
Direction L1: <<           Initial region span: 1-3,6-7,8-147 Gap history (edge excluded): 3-8 -> 3-6
Alt. candidates: [], []                                                                                           
Model 1BP/2BP comparison:  2BP vs 1BP: 7.23e-07                                                                   
Rec. model vs L1: 7.86e-16 Rec. model vs L2: 6.82e-52                                                      
Flags: Model_2BP_Best

XEC.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	3	4.681558	None	None	None	*	*	*

|||||

XEC.4.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4.1	68	6	11.014494	NaN	NaN	NaN	*	*	*
XEC.11	16	7	6.286401	-13.713599	33.427198	4.007212e-07		*
XEC.25	13	7	6.286401	-13.713599	33.427198	4.007212e-07		*
XEC.4.3	10	7	6.286401	-13.713599	33.427198	4.007212e-07		*
XEC.4.1.4	23	7	6.286401	-13.713599	33.427198	4.007212e-07		*
XEC.4	192	7	6.286401	-13.713599	33.427198	4.007212e-07		*
XEC.38	34	7	6.286401	-13.713599	33.427198	4.007212e-07		*
XEC.36	30	7	6.286401	-13.713599	33.427198	4.007212e-07		*
XEC.35.1	28	7	6.286401	-13.713599	33.427198	4.007212e-07		*
XEC.34	22	7	6.286401	-13.713599	33.427198	4.007212e-07		*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	8	239.111912	NaN	NaN	NaN	*	*	*
XEC.14	193	7	227.764683	226.984367	-149.968735	1.059816e-07		*
XEC.39	155	7	224.435789	223.894404	-143.788808	4.822372e-09		*
XEC.36	30	7	223.999669	212.432088	-120.864175	5.059114e-14		*
XEC.4	192	7	222.819634	211.236304	-118.472607	1.531414e-14		*
XEC.33	169	7	221.575180	209.983645	-115.967290	4.387574e-15		*
XEC.8	592	7	218.363432	206.738933	-109.477866	1.709774e-16		*
XEC.17	13	7	217.101708	205.534126	-107.068251	5.124057e-17		*
XEC.32	42	7	213.858612	202.291030	-100.582060	1.996772e-18		*
MC.24.1	25	7	213.494994	202.540517	-101.081034	2.563905e-18		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 936_C|T, 1711_T|C, 1714_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11137_T|A, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13665_C|T, 14408_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19524_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21411_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24382_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25453_A|C, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28775_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759, 29785_T|C

 Case 72 (XEC): USA/CA-LACPHL-AY11147/2025



Target: 5350 samples      Number of changes: 145                                                   
BC: XEC.33 + XEC.2        BC BR: 14-15                    BC BR coord: 7842 - 7843          
Direction L1: <<          Initial region span: 1-14,16-145 Gap history (edge excluded): 14-16
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 9.90e-01                                                            
Rec. model vs L1: 5.46e-32 Rec. model vs L2: 3.98e-24                                               
Flags: Model_1BP_Best

XEC.33 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.33	169	14	17.783166	NaN	NaN	NaN	*	*	*
XEC.4	192	14	17.681102	17.681102	-3.362204	9.003245e-01	*	*
XEC.16	23	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.4.3	10	12	15.079158	-7.384864	46.769728	1.171677e-11
XEC.32	42	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.17	13	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.22	23	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.18.3	13	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.24	11	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.25	13	12	15.079158	8.682101	14.635797	1.111089e-04	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	16	271.351893	NaN	NaN	NaN	*	*	*
XEC.14	193	28	245.024085	230.424664	-184.849328	3.710592e-14
XEC.29	135	16	242.299684	232.299684	-188.599368	2.419610e-13		*
XEC.25	13	28	237.617708	216.556357	-157.112714	3.513813e-20
XEC.30	135	28	234.867262	220.260406	-164.520813	1.428367e-18
XEC.2.1	265	28	229.985151	205.687253	-135.374506	6.683403e-25
XEC.5	126	28	227.124600	212.525180	-149.050360	6.245568e-22
XEC.18	165	28	226.505286	211.905866	-147.811731	3.359768e-22
XEC.9	305	24	225.734380	215.706172	-155.412344	1.501856e-20
XEC.39	155	5	223.777073	209.859526	-143.719052	4.346875e-23

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 915_A|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6638_C|T, 7842_A|G, 7852_T|C, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10273_T|C, 10447_G|A, 10449_C|A, 11042_G|T, 11200_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16308_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22594_C|T, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25613_C|T, 26060_C|T,
26093_A|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/CA-LACPHL-AY11224/2025



Target: 5350 samples      Number of changes: 147                                                   
BC: XEC.22 + KP.3.3       BC BR: 14-15                    BC BR coord: 7118 - 7119          
Direction L1: <<          Initial region span: 1-12,15-147 Gap history (edge excluded): 12-15
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 2.20e-03                                                            
Rec. model vs L1: 6.95e-48 Rec. model vs L2: 2.62e-18                                               
Flags: Model_1BP_Best

XEC.22 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.22	23	12	17.007649	NaN	NaN	NaN	*	*	*
XEC.24	11	11	11.469367	-4.920842	41.841683	1.791576e-07		*
XEC.8.1	12	11	11.469367	-5.007853	42.015706	1.637377e-07		*
XEC.32	42	11	11.469367	-4.920842	41.841683	1.791576e-07		*
XEC.16	23	11	11.469367	-4.920842	41.841683	1.791576e-07		*
XEC.17	13	11	11.469367	-4.920842	41.841683	1.791576e-07		*
XEC.25	13	11	11.469367	-4.920842	41.841683	1.791576e-07		*
XEC.4.3	10	11	11.469367	-11.575692	55.151383	2.306776e-10		*
XEC.18.3	13	11	11.469367	-4.920842	41.841683	1.791576e-07		*
XEC.4.1.4	23	11	11.469367	-16.646216	65.292432	1.449214e-12		*

|||||

KP.3.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.3	1715	15	228.780238	NaN	NaN	NaN	*	*	*
XEC.2	921	14	224.859125	221.262449	-166.524898	5.421326e-04	*	*
XEC.18	165	14	218.824983	215.215192	-154.430383	1.284681e-06		*
XEC.8	592	14	204.873712	201.263921	-126.527842	1.123020e-12		*
XEK.1	88	15	203.910097	203.910097	-131.820193	1.581598e-11		*
XEC.2.2	273	14	203.658322	200.048531	-124.097062	3.332112e-13		*
XEC.31	66	14	202.279959	198.670168	-121.340337	8.382878e-14		*
XEC.28	39	14	201.637429	198.027638	-120.055277	4.420228e-14		*
XEC.19	59	14	201.386508	197.776717	-119.553434	3.425308e-14		*
XEC.14	193	14	201.348784	197.738993	-119.477985	3.307496e-14		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1715_A|G, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4810_C|T, 5012_G|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11398_T|C, 11727_G|A, 12781_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22498_C|T, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24912_C|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25542_T|C, 25584_C|T, 25606_G|A,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27532_C|T, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29422_G|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/CA-LACPHL-AY11296/2025



Target: 5350 samples       Number of changes: 140                                               
BC: XEC.4 + BF.5.2         BC BR: 137-138                    BC BR coord: 28958 - 28959  
Direction L1: >>           Initial region span: 1-137,138-140 Gap history (edge excluded):
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 5.25e-09 Rec. model vs L2: 0.00e+00                                           
Flags: Model_2BP_Bad_L1_opp

XEC.4 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4	192	137	288.911961	NaN	NaN	NaN	*	*	*
XEC.18	165	137	284.454555	284.454555	-276.909110	1.162032e-02	*	*
XEC.8	592	140	277.301170	272.920885	-253.841771	1.136662e-07
MC.24.1	25	137	276.706342	276.706342	-261.412684	5.005366e-06		*
XEC.9	305	137	273.619054	273.619054	-255.238108	2.288956e-07		*
XEC.19	59	137	273.331153	273.331153	-254.662307	1.712742e-07		*
XEC.30	135	137	271.256368	271.256368	-250.512736	2.150458e-08		*
XEC.32	42	137	271.190311	271.190311	-250.380622	2.015124e-08		*
XEC.2	921	140	270.164997	265.683259	-239.366518	8.194277e-11
XEC.36	30	137	267.200870	267.200870	-242.401739	3.727922e-10		*

|||||

BF.5.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
BF.5.2	12	138	8.862472	NaN	NaN	NaN	*	*	*
BA.5.12	97	138	8.485647	8.485647	-10.971293	0.687289	*	*
ER.1.1	61	138	6.859675	6.859675	-7.719350	0.135335	*	*
XEK.1	88	138	6.359561	6.359561	-6.719122	0.082085	*	*
BF.11.1	311	138	6.260167	6.260167	-6.520334	0.074274	*	*
MC.10.2.1	11	138	6.233135	6.233135	-6.466269	0.072440	*	*
CJ.1.2	100	138	6.226827	6.226827	-6.453655	0.071719	*	*
ML.1	13	138	6.217480	6.217480	-6.434961	0.071005	*	*
XDY.6	11	138	6.099603	6.099603	-6.199207	0.063292	*	*
XBB.1.5.106	16	138	5.969256	5.969256	-5.938511	0.055576	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 2939_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5704_G|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G,
18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21575_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T,
22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A,
23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A,
29077_C|T, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/CA-LACPHL-AY11453/2025



Target: 5350 samples      Number of changes: 146                                                   
BC: XEC.4 + XEC.2         BC BR: 12-13                    BC BR coord: 4387 - 4388          
Direction L1: <<          Initial region span: 1-12,26-146 Gap history (edge excluded): 12-26
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 1.33e-01                                                            
Rec. model vs L1: 4.25e-26 Rec. model vs L2: 9.34e-25                                               
Flags: Model_1BP_Best

XEC.4 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4	192	12	24.875579	NaN	NaN	NaN	*	*	*
XEC.25	13	6	17.475308	16.862247	-7.724494	3.304682e-04	*
KP.3.1.1	12013	24	16.601492	10.301168	5.397665	4.679053e-07
XEC.18	165	12	15.393039	15.393039	-4.786078	7.636394e-05	*	*
MC.24.1	25	12	15.369184	15.369184	-4.738367	7.447850e-05	*	*
XEC.19	59	12	14.459938	14.459938	-2.919875	2.997940e-05	*	*
XEC.9	305	6	13.184990	12.525087	0.949825	4.329753e-06
XEC.8	592	6	13.170579	12.516266	0.967467	4.286672e-06
KP.3.1.12	39	4	11.473441	-7.416719	40.833437	9.476134e-15
JN.1	17255	16	10.826448	4.879750	16.240501	2.071485e-09

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	26	256.615521	NaN	NaN	NaN	*	*	*
XEC.29	135	26	248.908513	201.011461	-112.022921	9.291656e-19		*
XEC.31	66	26	245.197181	211.304463	-132.608926	2.748874e-14		*
XEC.33	169	29	239.796743	201.045862	-112.091724	9.622622e-19
XEC.8	592	26	239.523761	215.185122	-140.370245	1.331121e-12		*
KP.3.3	1715	8	236.865542	227.512277	-165.024554	2.998450e-07
XEC.2.2	273	26	236.634910	195.099581	-100.199163	2.520071e-21		*
XEC.9	305	26	236.238169	196.262636	-102.525271	8.079152e-21		*
XEC.14	193	26	235.597621	201.704903	-113.409807	1.861777e-18		*
XEK.5	28	26	235.525893	182.299674	-74.599348	6.957342e-27		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1102_C|T, 2060_G|A, 2790_C|T, 2939_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5784_C|T, 6183_A|G, 6361_C|T, 7842_A|G, 7865_G|T, 8293_C|T, 8393_G|A,
8950_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10093_T|A, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20483_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29272_C|T, 29510_A|C, 29670_C|T, 29734_29759

 Case 72 (XEC): USA/CA-LACPHL-AY11538/2025



Target: 5350 samples      Number of changes: 145                                                             
BC: XEC.2 + XEC.9 + XEC.2 BC BR: 4-5, 14-15                   BC BR coord: 896 - 897, 6026 - 6027     
Direction L1: <<          Initial region span: 1-4,6-14,15-145 Gap history (edge excluded): 4-15 -> 4-6
Alt. candidates: [], []                                                                                             
Model 1BP/2BP comparison: 2BP vs 1BP: 2.71e-05                                                                      
Rec. model vs L1: 1.20e-23 Rec. model vs L2: 2.75e-33                                                         
Flags: Model_2BP_Best

XEC.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	4	3.75823	None	None	None	*	*	*

|||||

XEC.9 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.9	305	6	18.888817	NaN	NaN	NaN	*	*	*
KP.3.1.10	51	8	16.450958	-18.842803	59.685607	9.012443e-13
JN.1.7.1	120	8	15.377918	-14.622082	51.244164	6.162213e-11
KP.3.3	1715	8	14.119585	-4.150811	30.301622	2.171701e-06
JN.1.10	28	8	13.952536	-16.047464	54.094928	1.482064e-11
MC.10.1	650	7	13.877320	-6.122680	34.245360	3.013480e-07		*
MC.1	932	7	13.850540	-6.149460	34.298920	2.939077e-07		*
MU.2.1	37	8	13.759752	-16.240248	54.480495	1.219494e-11
KP.1.1	593	7	13.364870	-6.635130	35.270261	1.809582e-07		*
JN.1.32.1	55	8	13.335346	-16.664654	55.329309	7.972683e-12

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	15	287.015305	NaN	NaN	NaN	*	*	*
KP.3.3	1715	8	274.513147	264.627067	-241.254135	4.397434e-12
XEC.4	192	6	259.202657	245.070275	-202.140550	1.414395e-20
XEC.39	155	16	257.129964	241.835838	-195.671675	5.567088e-22		*
XEC.32	42	8	256.167762	250.422434	-212.844868	2.978833e-18
XEC.9	305	6	255.461779	231.255438	-174.510876	1.415117e-26
XEC.29	135	17	252.990085	232.755617	-177.511235	6.342116e-26
XEK.1	88	17	243.910097	227.840467	-167.680934	4.652397e-28
XEC.2.2	273	16	243.658322	228.340171	-168.680343	7.670506e-28		*
XEC.31	66	16	242.279959	226.968244	-165.936488	1.949129e-28		*

Target sequence

, 241_C|T, 337_C|T, 670_T|G, 897_C|A, 1738_G|T, 2060_G|A, 2113_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5221_C|T, 6027_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12781_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23593_G|C, 23599_T|G, 23601_C|A, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25521_C|T, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/CA-LACPHL-AY12004/2025



Target: 5350 samples       Number of changes: 141                                               
BC: KP.2.5 + XEC.14        BC BR: 3-4                    BC BR coord: 678 - 679          
Direction L1: <<           Initial region span: 1-3,5-141 Gap history (edge excluded): 3-5
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 7.13e-145 Rec. model vs L2: 1.66e-17                                           
Flags: Model_2BP_Bad_L1_opp

KP.2.5 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.5	66	3	9.391444	NaN	NaN	NaN	*	*	*
CM.3	22	3	6.639909	6.639909	-7.279818	0.063928	*	*
BQ.1.1.7	1146	4	6.349948	2.677297	0.645407	0.001213	*	*
KP.5	77	3	6.000082	6.000082	-6.000164	0.033709	*	*
BN.1.2.3	117	3	5.653341	5.653341	-5.306682	0.023873	*	*
BQ.1.26	121	3	5.611641	5.611641	-5.223282	0.022823	*	*
BA.5.2.48	267	3	5.234796	5.234796	-4.469593	0.015686	*	*
BF.7.24	444	3	4.319240	4.319240	-2.638479	0.006282	*	*
BQ.1.11	1938	3	3.937737	3.937737	-1.875474	0.004296	*	*
BF.3	355	3	3.844681	3.844681	-1.689363	0.003907	*	*

|||||

XEC.14 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.14	193	5	276.499648	NaN	NaN	NaN	*	*	*
XEC.8	592	5	271.990858	261.990858	-225.981716	1.099846e-02	*	*
XEC.9	305	5	269.837039	259.837039	-221.674078	1.274757e-03	*	*
XEC.3	29	8	264.226759	254.140514	-210.281029	4.286672e-06
XEC.13	30	8	262.691703	252.605458	-207.210917	9.235878e-07
XEC.29	135	16	261.793841	241.762275	-185.524550	1.801169e-11
XEC.2	921	16	261.562400	231.368682	-164.737365	5.536494e-16
XEC.18	165	8	259.889050	249.790648	-201.581295	5.532727e-08
XEC.33	169	8	257.721668	247.605535	-197.211071	6.223085e-09
XEC.30	135	8	256.872574	246.748818	-195.497635	2.646574e-09

Target sequence

, 241_C|T, 592_T|C, 670_T|G, 875_C|A, 897_C|A, 2060_G|A, 2644_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6912_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11020_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/CA-LACPHL-AY12040/2025



Target: 5350 samples      Number of changes: 145                                                   
BC: XEC.4 + XEC.2         BC BR: 12-13                    BC BR coord: 4387 - 4388          
Direction L1: <<          Initial region span: 1-12,26-145 Gap history (edge excluded): 12-26
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 1.33e-01                                                            
Rec. model vs L1: 4.25e-26 Rec. model vs L2: 9.34e-25                                               
Flags: Model_1BP_Best

XEC.4 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4	192	12	24.875579	NaN	NaN	NaN	*	*	*
XEC.25	13	6	17.475308	16.862247	-7.724494	3.304682e-04	*
KP.3.1.1	12013	24	16.601492	10.301168	5.397665	4.679053e-07
XEC.18	165	12	15.393039	15.393039	-4.786078	7.636394e-05	*	*
MC.24.1	25	12	15.369184	15.369184	-4.738367	7.447850e-05	*	*
XEC.19	59	12	14.459938	14.459938	-2.919875	2.997940e-05	*	*
XEC.9	305	6	13.184990	12.525087	0.949825	4.329753e-06
XEC.8	592	6	13.170579	12.516266	0.967467	4.286672e-06
KP.3.1.12	39	4	11.473441	-7.416719	40.833437	9.476134e-15
JN.1	17255	16	10.826448	4.879750	16.240501	2.071485e-09

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	26	266.615521	NaN	NaN	NaN	*	*	*
XEC.29	135	26	258.908513	211.011461	-134.022921	9.291656e-19		*
XEC.31	66	26	255.197181	221.304463	-154.608926	2.748874e-14		*
XEC.33	169	29	249.796743	211.045862	-134.091724	9.622622e-19
XEC.8	592	26	249.523761	225.185122	-162.370245	1.331121e-12		*
KP.3.3	1715	8	246.865542	237.512277	-187.024554	2.998450e-07
XEC.2.2	273	26	246.634910	205.099581	-122.199163	2.520071e-21		*
XEC.9	305	26	246.238169	206.262636	-124.525271	8.079152e-21		*
XEC.14	193	26	245.597621	211.704903	-135.409807	1.861777e-18		*
XEK.5	28	26	245.525893	192.299674	-96.599348	6.957342e-27		*

Target sequence

 Case 72 (XEC): USA/CA-LACPHL-AY12077/2025



Target: 5350 samples      Number of changes: 147                                                   
BC: XEC.5 + XEC.2         BC BR: 13-14                    BC BR coord: 4387 - 4388          
Direction L1: <<          Initial region span: 1-10,15-147 Gap history (edge excluded): 10-15
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 1.35e-01                                                            
Rec. model vs L1: 1.29e-28 Rec. model vs L2: 4.90e-25                                               
Flags: Model_1BP_Best

XEC.5 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.5	126	10	14.842864	NaN	NaN	NaN	*	*	*
XEC.33	169	10	13.426664	5.573522	20.852955	2.465970e-01	*	*
XEC.15	127	10	12.993314	5.140172	21.719657	1.596135e-01	*	*
MC.1.2	49	4	11.386334	-8.149519	48.299037	2.699579e-07
MA.1.2	96	4	9.978552	-9.557301	51.114601	6.623876e-08
KP.1.1.1	578	4	8.185275	-11.396450	54.792900	1.051987e-08
LP.8.1.1	2345	4	6.779659	-19.354581	70.709161	3.673045e-12
JN.1	17255	4	4.792390	-4.820399	41.640799	7.542175e-06
MR.1	17	3	4.718819	-42.403648	116.807295	3.585407e-22
MC.17.1	10	3	4.718819	-24.922394	81.844788	1.406622e-14

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	15	235.334694	NaN	NaN	NaN	*	*	*
XEC.9	305	16	235.222128	222.749103	-155.498207	7.539608e-02	*	*
XEC.33	169	5	230.952196	220.067605	-150.135210	5.169393e-03	*
XEC.8	592	26	218.593270	205.772722	-121.545444	3.200368e-09
XEC.2.2	273	26	215.557666	195.099581	-100.199163	7.397864e-14
XEC.29	135	26	215.472903	188.653095	-87.306190	1.175110e-16
XEC.2.1	265	26	215.367090	192.845563	-95.691126	7.758402e-15
XEC.14	193	26	214.520377	201.704903	-113.409807	5.465393e-11
XEK.5	28	26	214.448649	182.299674	-74.599348	2.042382e-19
XEC.31	66	26	211.045951	198.230477	-106.460955	1.692186e-12

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 919_A|G, 2060_G|A, 2790_C|T, 3037_C|T, 3061_A|G, 3431_G|T, 3565_T|C, 3879_A|G, 4184_G|A, 4321_C|T, 5193_T|A, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 9711_C|T, 10029_C|T, 10198_C|T, 10432_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15614_A|G,
15714_C|T, 15746_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24038_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25521_C|G,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28723_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/DC-CDC-2-8448731/2025



Target: 5350 samples      Number of changes: 146                                                   
BC: XEC.33 + XEC.2        BC BR: 15-16                    BC BR coord: 6183 - 6184          
Direction L1: <<          Initial region span: 1-12,18-146 Gap history (edge excluded): 12-18
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 4.76e-06                                                            
Rec. model vs L1: 5.15e-09 Rec. model vs L2: 5.20e-19                                               
Flags: Model_1BP_Best

XEC.33 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.33	169	12	13.225069	NaN	NaN	NaN	*	*	*
XEC.17	13	11	11.469367	-14.920842	59.841683	0.000008		*
XEC.25	13	11	11.469367	-14.920842	59.841683	0.000008		*
XEC.24	11	11	11.469367	-14.920842	59.841683	0.000008		*
XEC.8.1	12	11	11.469367	-15.007853	60.015706	0.000007		*
XEC.22	23	11	11.469367	-14.920842	59.841683	0.000008		*
XEC.4.3	10	11	11.469367	-14.920842	59.841683	0.000008		*
XEC.18.3	13	11	11.469367	-14.920842	59.841683	0.000008		*
XEC.16	23	11	11.469367	-14.920842	59.841683	0.000008		*
XEC.32	42	11	11.469367	-14.920842	59.841683	0.000008		*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	18	245.978085	NaN	NaN	NaN	*	*	*
KP.3.3	1715	16	242.468094	238.091834	-190.183667	2.253727e-01	*
XEC.9	305	18	235.063472	222.583600	-159.167199	4.160689e-08		*
XEC.33	169	29	229.910330	221.143900	-156.287799	9.857828e-09
XEK.1.2	33	20	218.719356	198.546170	-111.092339	1.509128e-18
XEC.8	592	18	215.457227	209.058479	-132.116959	5.563299e-14		*
XEC.4.6.1	13	16	212.670454	206.015604	-126.031208	2.647925e-15
XEC.31	66	18	212.585065	206.188008	-126.376017	3.154331e-15		*
XEC.28	39	18	212.119082	205.722025	-125.444049	1.971464e-15		*
XEC.29	135	18	212.078102	197.117967	-108.235935	3.629579e-19		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1879_A|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4543_C|T, 5164_G|T, 6040_C|T, 6183_A|G, 7842_A|G, 7844_C|T, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11173_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16393_C|T, 17410_C|T, 18163_A|G, 18401_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25799_A|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27630_C|T, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29101_A|G, 29510_A|C

 Case 72 (XEC): USA/DE-CDC-LC1136200/2025



Target: 5350 samples       Number of changes: 143                                               
BC: XEC.32 + LZ.5          BC BR: 140-141                    BC BR coord: 28958 - 28959  
Direction L1: >>           Initial region span: 1-140,141-143 Gap history (edge excluded):
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 8.36e-09 Rec. model vs L2: 1.63e-101                                          
Flags: Model_2BP_Bad_L1_opp

XEC.32 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.32	42	140	256.256839	NaN	NaN	NaN	*	*	*
KP.3.3	1715	143	248.731067	245.653078	-191.306156	2.491601e-05	*
XEC.19	59	140	247.191129	247.191129	-194.382257	1.156433e-04	*	*
XEC.39	155	140	246.656679	246.656679	-193.313357	6.772874e-05	*	*
XEC.8	592	143	244.989738	241.025281	-182.050563	2.430497e-07
XEC.9	305	143	240.935604	234.766363	-169.532725	4.645277e-10
XEC.11	16	140	240.829204	240.829204	-181.658409	1.999897e-07		*
XEC.36	30	140	240.613602	240.613602	-181.227203	1.613000e-07		*
XEC.17	13	140	239.424370	239.424370	-178.848739	4.907088e-08		*
XEC.24	11	127	239.053640	235.194571	-170.389142	7.140986e-10

|||||

LZ.5 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LZ.5	14	141	8.697959	NaN	NaN	NaN	*	*	*
BQ.1.33	11	141	7.293213	7.293213	-8.586427	0.245367	*	*
XBB.1.4	50	141	7.104036	7.104036	-8.208073	0.202909	*	*
HN.3	27	141	6.644733	6.644733	-7.289465	0.128093	*	*
XEC.27	25	141	6.526721	6.526721	-7.053442	0.113608	*	*
JN.1.7.7	13	141	6.448280	6.448280	-6.896559	0.105399	*	*
XBB.1.5.89	23	141	6.348644	6.348644	-6.697287	0.095369	*	*
BF.5.4	14	141	6.213052	6.213052	-6.426105	0.083326	*	*
XEC.9	305	141	6.169241	6.169241	-6.338482	0.079659	*	*
HN.7	28	141	6.066449	6.066449	-6.132898	0.071719	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4475_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 10978_A|G, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G,
18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22367_T|C, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T,
22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A,
23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25099_T|C, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T,
26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27549_C|T, 27807_C|T, 27810_T|C, 28093_C|T, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29420_C|T, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/DE-USAFSAM-S23724/2025



Target: 5350 samples       Number of changes: 141                                               
BC: XEC.32 + LZ.5          BC BR: 138-139                    BC BR coord: 28958 - 28959  
Direction L1: >>           Initial region span: 1-138,139-141 Gap history (edge excluded):
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 8.32e-09 Rec. model vs L2: 9.36e-101                                          
Flags: Model_2BP_Bad_L1_opp

XEC.32 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.32	42	138	258.687290	NaN	NaN	NaN	*	*	*
KP.3.3	1715	141	255.114028	252.036038	-206.072077	1.294022e-03	*
XEC.19	59	138	253.833234	253.833234	-209.666467	7.828378e-03	*	*
XEC.8	592	141	251.478482	247.514026	-197.028051	1.409064e-05	*
XEC.39	155	138	249.274098	249.274098	-200.548196	8.190095e-05	*	*
XEC.9	305	141	247.346353	241.177111	-184.354223	2.486014e-08
XEC.14	193	141	243.834503	239.020505	-180.041010	2.881370e-09
XEC.11	16	138	243.526719	243.526719	-189.053437	2.606728e-07		*
XEC.36	30	138	243.100395	243.100395	-188.200790	1.704200e-07		*
XEC.4	192	138	242.050643	242.050643	-186.101287	5.963638e-08		*

|||||

LZ.5 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LZ.5	14	139	8.697959	NaN	NaN	NaN	*	*	*
BQ.1.33	11	139	7.293213	7.293213	-8.586427	0.245367	*	*
XBB.1.4	50	139	7.104036	7.104036	-8.208073	0.202909	*	*
HN.3	27	139	6.644733	6.644733	-7.289465	0.128093	*	*
XEC.27	25	139	6.526721	6.526721	-7.053442	0.113608	*	*
JN.1.7.7	13	139	6.448280	6.448280	-6.896559	0.105399	*	*
XBB.1.5.89	23	139	6.348644	6.348644	-6.697287	0.095369	*	*
BF.5.4	14	139	6.213052	6.213052	-6.426105	0.083326	*	*
XEC.9	305	139	6.169241	6.169241	-6.338482	0.079659	*	*
HN.7	28	139	6.066449	6.066449	-6.132898	0.071719	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4475_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 10978_A|G, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G,
18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994,
22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22367_T|C, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T,
26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27549_C|T, 27807_C|T, 27810_T|C, 28093_C|T, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28958_C|A, 29420_C|T, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/FL-CDC-LC1136791/2025



Target: 5350 samples       Number of changes: 146                                                   
BC: KP.3.1.1 + XEC.25      BC BR: 29-30                    BC BR coord: 10520 - 10521        
Direction L1: <<           Initial region span: 1-15,30-146 Gap history (edge excluded): 15-30
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 4.96e-74 Rec. model vs L2: 2.08e-18                                               
Flags: Model_2BP_Bad_L1_opp

KP.3.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.1	12013	15	13.768491	NaN	NaN	NaN	*	*	*
BF.11	2573	4	8.632640	-98.631561	281.263121	8.444995e-42
XEC.29	135	9	7.073173	-30.572888	145.145776	3.037458e-12
BF.11.2	418	3	6.710957	-154.574374	393.148748	4.265742e-66
BF.11.1	311	3	6.709306	-136.718397	357.436794	2.422828e-58
BF.11.5	122	3	6.707517	-164.682541	413.365082	1.734912e-70
BF.11.4	202	3	6.700834	-142.814352	369.628704	5.461321e-61
NY.16	136	5	6.305066	-56.928874	197.857749	1.088126e-23
KP.3.3.1	211	5	6.159968	-25.195072	134.390145	6.591961e-10
JN.1.9	576	5	5.965395	-34.571607	153.143213	5.591185e-14

|||||

XEC.25 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.25	13	30	258.133541	NaN	NaN	NaN	*	*	*
XEC.8	592	30	257.929424	257.929424	-275.858849	8.146473e-01	*	*
XEC.9	305	30	255.586242	255.586242	-271.172484	7.808167e-02	*	*
XEC.2	921	30	254.855862	254.855862	-269.711724	3.762826e-02	*	*
XEC.40	52	30	250.218231	250.218231	-260.436463	3.652239e-04	*	*
XEC.31	66	17	245.529196	243.254953	-246.509905	3.449039e-07
KP.3.3	1715	30	245.265231	245.265231	-250.530462	2.574127e-06		*
XEK.1	88	30	243.126897	243.126897	-246.253794	3.028585e-07		*
XEC.2.1	265	30	242.933619	242.933619	-245.867237	2.504516e-07		*
XEC.29	135	30	242.822062	242.822062	-245.644123	2.232441e-07		*

Target sequence

, 140_C|T, 241_C|T, 670_T|G, 835_C|T, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3448_C|T, 3565_T|C, 4184_G|A, 4321_C|T, 5826_C|T, 6183_A|G, 6607_T|C, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 9556_T|C, 10029_C|T, 10198_C|T, 10416_C|T, 10447_G|A, 10449_C|A, 10519_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19497_T|C, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 21998_C|T, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/IL-RIPHL_124021_G/2025



Target: 5350 samples       Number of changes: 145                                               
BC: KP.2.2 + XEC.2         BC BR: 5-6                    BC BR coord: 1713 - 1714        
Direction L1: <<           Initial region span: 1-5,7-145 Gap history (edge excluded): 5-7
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 1.09e-87 Rec. model vs L2: 1.05e-11                                           
Flags: Model_2BP_Bad_L1_opp

KP.2.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.2	1334	5	9.029481	NaN	NaN	NaN	*	*	*
KW.1.1	127	4	7.613024	-2.386976	16.773953	1.102881e-05	*	*
MC.43	131	4	7.599120	-2.400880	16.801761	1.086461e-05	*	*
CL.1	688	3	7.215446	-12.784554	37.569109	3.356339e-10
JN.1.1	3081	4	7.081387	-2.918613	17.837226	6.459233e-06		*
KP.3.3	1715	4	6.628465	-3.371535	18.743070	4.118589e-06		*
JN.1.19	438	4	6.390614	-10.400399	32.800797	3.644670e-09		*
MC.16	917	4	6.354086	-3.645914	19.291828	3.128365e-06		*
MC.1	932	4	6.314172	-3.685828	19.371655	3.005700e-06		*
KP.2.3	4440	4	6.021946	-3.978054	19.956108	2.237839e-06		*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	7	249.082219	NaN	NaN	NaN	*	*	*
XEC.39	155	6	234.435789	234.435789	-170.871578	9.609530e-03	*	*
XEC.14	193	6	228.083666	228.083666	-158.167331	1.678542e-05	*	*
XEC.17	13	6	227.101708	227.101708	-156.203415	6.268334e-06		*
XEC.15	127	6	224.274571	224.274571	-150.549141	3.717665e-07		*
XEC.32	42	6	223.858612	223.858612	-149.717224	2.454924e-07		*
MC.24.1	25	6	223.494994	223.494994	-148.989989	1.704200e-07		*
XEC.4	192	6	223.133422	223.133422	-148.266844	1.188980e-07		*
XEC.38	34	6	223.036607	223.036607	-148.073214	1.075833e-07		*
XEC.24	11	6	222.871909	222.871909	-147.743818	9.121924e-08		*

Target sequence

, 241_C|T, 443_G|A, 670_T|G, 897_C|A, 1711_T|C, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4927_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 8412_A|G, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11137_T|A, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13665_C|T, 14408_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21411_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25453_A|C, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759, 29785_T|C

 Case 72 (XEC): USA/IL-RIPHL_124096_G/2025



Target: 5350 samples       Number of changes: 147                                                 
BC: KP.2.3.7 + XEC.14      BC BR: 6-7                     BC BR coord: 1651 - 1652         
Direction L1: <<           Initial region span: 1-6,11-147 Gap history (edge excluded): 6-11
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  1BP vs 2BP: 2.03e-01                                                          
Rec. model vs L1: 1.73e-154 Rec. model vs L2: 5.05e-17                                             
Flags: Model_1BP_Best

KP.2.3.7 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3.7	54	6	16.853608	NaN	NaN	NaN	*	*	*
XEC.11.1	166	9	14.746054	7.378559	-0.757117	7.674671e-05	*
JN.1.53	62	6	14.228038	14.228038	-14.456075	7.243976e-02	*	*
KP.5	77	6	13.906467	13.906467	-13.812933	5.233971e-02	*	*
KP.3.3.3	288	6	12.833681	12.833681	-11.667362	1.795296e-02	*	*
LA.1	149	6	12.440820	12.440820	-10.881641	1.209455e-02	*	*
LF.7.9.3	20	5	11.825673	1.825673	10.348653	2.968615e-07		*
XFB.3	56	5	11.670112	1.670112	10.659776	2.542367e-07		*
XEL.5	19	5	11.593891	1.593891	10.812218	2.358665e-07		*
LC.1	10	5	11.297148	1.297148	11.405704	1.747342e-07		*

|||||

XEC.14 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.14	193	11	234.385154	NaN	NaN	NaN	*	*	*
KP.3.3	1715	11	229.858678	222.667042	-127.334083	1.127881e-04	*	*
XEC.17	13	11	219.734212	217.101708	-116.203415	4.319310e-07		*
XEC.21	38	11	219.337069	208.969159	-99.938317	1.272331e-10		*
XEC.31	66	41	219.196756	211.092222	-104.184444	1.059997e-09
XEC.40	52	41	219.182933	205.054631	-92.109262	2.537099e-12
XEK.1	88	41	219.068700	167.385281	-16.770562	1.107807e-28
XEC.2.1	265	41	218.882998	184.871171	-51.742343	4.346135e-21
XEC.25	13	41	218.792918	212.084697	-106.169394	2.866999e-09
XEC.29	135	41	218.771300	204.570922	-91.141843	1.562084e-12

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1651_T|C, 2060_G|A, 2790_C|T, 3037_C|T, 3379_A|G, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9220_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12669_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 12965_T|C, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 17172_C|A, 17343_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G,
22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A,
23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
25603_C|A, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29109_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/IL-RIPHL_124110_G/2025



Target: 5350 samples       Number of changes: 145                                               
BC: KP.2.3.7 + XEC.14      BC BR: 4-5                    BC BR coord: 1651 - 1652        
Direction L1: <<           Initial region span: 1-4,9-145 Gap history (edge excluded): 4-9
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 1.73e-154 Rec. model vs L2: 3.47e-17                                           
Flags: Model_2BP_Bad_L1_opp

KP.2.3.7 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3.7	54	4	13.173619	NaN	NaN	NaN	*	*	*
XEC.11.1	166	7	11.010599	3.643104	2.713793	0.000073	*
JN.1.53	62	4	10.131202	10.131202	-10.262404	0.047596	*	*
KP.5	77	4	9.783441	9.783441	-9.566882	0.033709	*	*
LA.1	149	4	9.250311	9.250311	-8.500622	0.019742	*	*
KP.3.3.3	288	4	8.580112	8.580112	-7.160223	0.010102	*	*
JN.1.9	576	4	7.897534	7.897534	-5.795069	0.005118	*	*
KP.2.3	4440	4	7.454984	7.454984	-4.909967	0.003280	*	*
LP.8.1.1	2345	4	6.469249	6.469249	-2.938498	0.001225	*	*
JN.1.1	3081	4	6.211840	6.211840	-2.423679	0.000944	*	*

|||||

XEC.14 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.14	193	9	234.385154	NaN	NaN	NaN	*	*	*
KP.3.3	1715	9	229.858678	222.667042	-127.334083	1.127881e-04	*	*
XEC.17	13	9	219.734212	217.101708	-116.203415	4.319310e-07		*
XEC.21	38	9	219.337069	208.969159	-99.938317	1.272331e-10		*
XEC.31	66	39	219.196756	211.092222	-104.184444	1.059997e-09
XEC.40	52	39	219.182933	205.054631	-92.109262	2.537099e-12
XEK.1	88	39	219.068700	167.385281	-16.770562	1.107807e-28
XEC.2.1	265	39	218.882998	184.871171	-51.742343	4.346135e-21
XEC.25	13	39	218.792918	212.084697	-106.169394	2.866999e-09
XEC.29	135	39	218.771300	204.570922	-91.141843	1.562084e-12

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1651_T|C, 2060_G|A, 2790_C|T, 3037_C|T, 3379_A|G, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9220_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12669_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 12965_T|C, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
17172_C|A, 17343_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25603_C|A, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29109_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/IL-RIPHL_124115_G/2025



Target: 5350 samples       Number of changes: 144                                               
BC: JN.1.61 + XEC.2        BC BR: 4-5                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-4,7-144 Gap history (edge excluded): 4-7
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 5.80e-100 Rec. model vs L2: 7.00e-08                                           
Flags: Model_2BP_Bad_L1_opp

JN.1.61 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.61	13	4	12.830988	NaN	NaN	NaN	*	*	*
JN.1.31	204	4	11.399343	11.399343	-12.798685	2.393089e-01	*	*
MC.3	68	4	11.146800	11.146800	-12.293599	1.854444e-01	*	*
BF.10.1	37	3	8.157665	-1.842335	13.684670	4.255004e-07		*
BA.5	6418	3	5.390395	-4.609605	19.219209	2.666271e-08		*
BA.4.6	19369	3	3.683843	-10.215003	30.430006	9.810331e-11		*
BA.5.1.22	4997	3	3.240544	-6.759456	23.518912	3.105783e-09		*
XEC.25	13	5	1.005220	-5.281181	20.562362	1.364354e-08		*
XEC.24	11	5	1.005220	-5.281181	20.562362	1.364354e-08		*
XEC.29	135	5	1.005220	-5.281181	20.562362	1.364354e-08		*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	7	254.773388	NaN	NaN	NaN	*	*	*
XEC.39	155	3	240.652038	235.950730	-171.901459	3.238143	*
XEC.25	13	3	240.255109	235.540855	-171.081710	2.148994	*
XEC.18	165	3	239.990716	235.288621	-170.577242	1.673639	*
XEC.33	169	3	237.817906	233.133541	-166.267082	0.193980	*
XEC.8	592	3	236.165715	231.520273	-163.040547	0.038581	*
XEC.17	13	3	231.815961	227.101708	-154.203415	0.000464	*
XEC.14	193	7	231.797265	228.083666	-156.167331	0.001243	*	*
XEC.15	127	3	230.743005	226.044625	-152.089250	0.000162	*
XEC.31	66	15	228.670168	221.092222	-142.184444	0.000001

Target sequence

, 241_C|T, 347_G|T, 670_T|G, 897_C|A, 2060_G|A, 2069_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6543_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18075_T|C,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25669_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G,
26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27795_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28352_A|G, 28362_28370, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29358_C|T, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/IL-USAFSAM-S23723/2025



Target: 5350 samples       Number of changes: 142                                                                  
BC: XEC.4 + JN.1.39 + XEC.4 BC BR: 11-12, 16-17                   BC BR coord: 4330 - 4331, 8292 - 8293      
Direction L1: <<           Initial region span: 1-11,13-16,17-142 Gap history (edge excluded): 11-17 -> 11-13
Alt. candidates: [], []                                                                                                   
Model 1BP/2BP comparison:  2BP vs 1BP: 9.45e-06                                                                           
Rec. model vs L1: 1.98e-12 Rec. model vs L2: 2.29e-86                                                              
Flags: Model_2BP_Best

XEC.4 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4	192	11	11.411059	None	None	None	*	*	*

|||||

JN.1.39 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.39	1007	13	9.471030	NaN	NaN	NaN	*	*	*
JN.1.4	8971	13	8.094207	-1.905793	21.811586	2.528396e-01	*	*
KS.1.1.2	252	15	8.088122	-14.898127	47.796254	5.743654e-07
MC.1	932	14	7.121538	-3.654406	25.308813	4.393693e-02	*	*
MC.1.3	51	15	7.120776	-13.656244	45.312488	1.994734e-06
NL.12	51	15	7.120776	-9.269433	36.538866	1.600539e-04	*
JN.1.7.4	101	15	7.120678	-9.269531	36.539062	1.600539e-04	*
JN.1.38.1	107	15	7.072920	-9.326679	36.653357	1.514886e-04	*
LP.8.1.5	168	15	7.027250	-25.461006	68.922012	1.489493e-11
JN.1	17255	13	6.967998	6.095705	5.808589	7.537042e+02	*	*

|||||

XEC.4 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4	192	17	261.385774	NaN	NaN	NaN	*	*	*
XEC.6	45	2	259.683711	259.423336	-226.846671	1.561287e-06
XEC.31	66	17	249.414537	260.838102	-229.676204	6.427017e-06		*
XEC.15	127	2	247.771080	248.556135	-205.112270	2.969626e-11
XEC.24	11	17	247.354286	258.823653	-225.647306	8.568525e-07		*
XEC.29	135	15	247.155609	252.455289	-212.910577	1.467068e-09
XEC.2.2	273	21	245.924553	240.926408	-189.852816	1.442231e-14
XEC.2	921	6	243.179137	235.579887	-179.159775	6.882257e-17
XEC.8	592	17	242.121633	253.469042	-214.938084	4.048174e-09		*
XEC.2.1	265	17	241.983075	237.093317	-182.186633	3.131028e-16		*

Target sequence

, 54_T|A, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4930_T|C, 6183_A|G, 7165_C|T, 7842_A|G, 8247_C|T, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21578_G|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21844_C|T,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25452_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G,
26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C,
28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/IVY-G25Y94R9/2025



Target: 5350 samples      Number of changes: 142                                                             
BC: XEC.2 + XEC.18 + XEC.2 BC BR: 3-4, 15-16                   BC BR coord: 896 - 897, 7841 - 7842     
Direction L1: <<          Initial region span: 1-3,5-15,16-142 Gap history (edge excluded): 3-16 -> 3-5
Alt. candidates: [], []                                                                                             
Model 1BP/2BP comparison: 2BP vs 1BP: 3.32e-02                                                                      
Rec. model vs L1: 1.29e-30 Rec. model vs L2: 3.16e-20                                                         
Flags: Model_2BP_Best

XEC.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	3	4.681558	None	None	None	*	*	*

|||||

XEC.18 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.18	165	5	14.256531	NaN	NaN	NaN	*	*	*
LF.7.9.3	20	14	9.958902	-25.945726	87.891452	7.661374e-14
XEC.24	11	5	8.798033	-1.201967	38.403935	4.274877e-03	*	*
LF.7.3.5	16	14	7.173478	-28.508007	93.016013	5.893066e-15
LF.7.9	20	14	6.963170	-28.823675	93.647351	4.300694e-15
PC.3.1	27	14	6.663065	-37.730533	111.461066	5.836415e-19
JN.1.41	121	14	6.549406	-11.185720	58.371441	1.970122e-07
XBB.1.5.97	39	15	6.349111	-60.422937	156.845874	8.125178e-29
B.1.474	13	15	6.349111	-106.473793	248.947586	8.139018e-49
GN.1.4	13	15	6.349111	-69.934752	175.869503	6.021329e-33

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	16	279.381372	NaN	NaN	NaN	*	*	*
XEC.18	165	5	266.714506	257.164636	-248.329272	2.077201e-12
XEC.24	11	5	261.309602	257.230389	-248.460778	2.216703e-12
XEC.31	66	16	258.670168	263.358453	-260.716905	1.018434e-09		*
XEC.29	135	16	258.229842	262.948662	-259.897323	6.758838e-10		*
XEC.9	305	16	258.101204	262.783680	-259.567361	5.730776e-10		*
XEC.28	39	16	258.027638	262.667838	-259.335677	5.108220e-10		*
XEC.19	59	16	257.776717	262.443350	-258.886701	4.078996e-10		*
XEC.14	193	16	257.738993	262.431674	-258.863348	4.018268e-10		*
XEC.17	13	16	256.741368	261.460188	-256.920375	1.523257e-10		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1218_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3482_G|A, 3565_T|C, 4184_G|A, 4321_C|T, 5926_T|C, 6183_A|G, 7834_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22927_G|T, 22928_T|C, 22942_T|A,
22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25435_T|C, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/IVY-G25Y98H5/2025



Target: 5350 samples       Number of changes: 143                                               
BC: XEC.15 + XEC.2         BC BR: 5-6                    BC BR coord: 2060 - 2061        
Direction L1: <<           Initial region span: 1-5,7-143 Gap history (edge excluded): 5-7
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 2.97e-19 Rec. model vs L2: 7.14e-16                                           
Flags: Model_2BP_Bad_L1_opp

XEC.15 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.15	127	5	12.808072	NaN	NaN	NaN	*	*	*
XEC.30	135	5	12.017272	12.017272	-12.034545	4.515812e-01	*	*
XEC.39	155	5	11.912143	11.912143	-11.824285	4.065697e-01	*	*
NM.2	28	4	10.652217	0.652217	10.695567	5.235752e-06		*
LP.7	57	4	10.477981	0.477981	11.044038	4.417220e-06		*
KP.2.24	44	4	9.583943	-0.416057	12.832113	1.804910e-06		*
MC.14	35	4	9.377846	-0.622154	13.244308	1.470365e-06		*
KP.2.3.13	25	4	8.568321	-1.431679	14.863359	6.541037e-07		*
JN.1.1.6	13	4	8.123635	-9.120888	30.241775	2.991727e-10		*
KP.3.4	62	4	7.931484	-2.068516	16.137033	3.449039e-07		*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	7	268.083499	NaN	NaN	NaN	*	*	*
XEC.8	592	2	259.645691	248.721177	-203.442354	8.567067e-05	*
XEC.36	30	2	250.053785	239.048565	-184.097130	5.410091e-09
XEC.17	13	2	241.820527	230.815307	-167.630613	1.434794e-12
XEC.14	193	7	241.797265	231.797265	-169.594529	3.822945e-12		*
XEC.2.2	273	15	240.070471	226.209990	-158.419980	1.435038e-14
XEC.31	66	15	238.670168	224.805821	-155.611642	3.521110e-15
XEC.32	42	2	238.577431	227.572211	-161.144422	5.591185e-14
XEC.29	135	15	238.229842	218.284521	-142.569041	5.188952e-18
MC.24.1	25	2	238.172992	227.862520	-161.725039	7.509668e-14

Target sequence

, 106_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2433_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6500_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16443_C|T, 17410_C|T,
18163_A|G, 18492_A|G, 18632_T|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22388_C|T, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22639_C|A, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/IVY-G25Z06J6/2025



Target: 5350 samples      Number of changes: 151                                                   
BC: XEC.33 + XEC.2        BC BR: 13-14                    BC BR coord: 6183 - 6184          
Direction L1: <<          Initial region span: 1-13,33-151 Gap history (edge excluded): 13-33
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 6.60e-01                                                            
Rec. model vs L1: 8.07e-34 Rec. model vs L2: 3.96e-24                                               
Flags: Model_1BP_Best

XEC.33 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.33	169	13	17.494146	NaN	NaN	NaN	*	*	*
KP.3.1.1	12013	13	14.119344	14.119344	3.761311	3.421812e-02	*	*
XEC.4.1.1	12	4	11.005220	-3.039664	38.079328	1.207154e-09
XEC.25	13	4	11.005220	5.079158	21.841683	4.057271e-06
XEC.4.1.4	23	4	11.005220	0.008634	31.982731	2.548948e-08
XEC.36	30	4	11.005220	5.045257	21.909486	3.917723e-06
XEC.32	42	4	11.005220	5.079158	21.841683	4.057271e-06
XEC.3	29	4	11.005220	5.044067	21.911866	3.917723e-06
XEC.29	135	4	11.005220	-0.377024	32.754048	1.734433e-08
XEC.27	25	4	11.005220	4.995777	22.008446	3.726653e-06

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	33	231.429180	NaN	NaN	NaN	*	*	*
XEC.39	155	46	225.103290	155.636125	-19.272251	3.062670e-21
XEC.31	66	46	218.124388	148.670168	-5.340337	2.892272e-24
XEC.40	52	46	218.110565	142.331001	7.337998	5.102841e-27
XEK.1	88	46	217.996332	149.523285	-7.046571	6.800813e-24
XEC.2.1	265	46	217.810630	138.650357	14.699285	1.287088e-28
XEC.25	13	46	217.720550	141.724358	8.551285	2.786531e-27
XEC.29	135	46	217.698932	149.602211	-7.204421	7.330489e-24
XEK.5	28	46	217.603736	137.364286	17.271427	3.560738e-29
XEC.33	169	46	217.580545	140.350438	11.299124	7.045454e-28

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2069_A|G, 2790_C|T, 2847_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7125_C|A, 7842_A|G, 8293_C|T, 8393_G|A, 8991_C|T, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10663_T|C, 11042_G|T, 11139_C|T, 11288_11296, 11727_G|A, 12213_C|T, 12427_T|C, 12781_C|T, 12789_C|T, 12815_C|T, 12880_C|T,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 15763_C|T, 17274_C|T, 17410_C|T, 18060_C|T, 18086_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G,
21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G,
22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T,
22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T,
24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25669_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27795_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/LA-CDC-2-8448566/2025



Target: 5350 samples       Number of changes: 146                                                 
BC: XEC.9 + XEC.2          BC BR: 12-13                   BC BR coord: 4387 - 4388         
Direction L1: <<           Initial region span: 1-9,13-146 Gap history (edge excluded): 9-13
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  -                                                                             
Rec. model vs L1: 5.51e-16 Rec. model vs L2: 7.29e-24                                             
Flags: Model_2BP_Bad_L1_opp

XEC.9 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.9	305	9	20.521588	NaN	NaN	NaN	*	*	*
KP.3.3	1715	12	17.382156	17.382156	-10.764313	111.608811	*
XEC.18	165	12	13.785538	13.785538	-3.571076	3.064854	*
XEC.15	127	12	12.887384	12.887384	-1.774768	1.246077	*
MC.24	831	9	12.803342	4.947791	14.104418	0.000446	*	*
KP.3.1	1957	9	11.763566	3.906842	16.186315	0.000157	*	*
KP.3.1.1	12013	12	11.308495	11.308495	1.383010	0.257947	*
LF.7.4	15	4	10.108672	0.429719	23.140563	0.000005
XEC.32	42	9	9.322509	1.469367	21.061265	0.000014	*	*
XEC.16	23	9	9.322509	1.469367	21.061265	0.000014	*	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	13	221.423823	NaN	NaN	NaN	*	*	*
XEC.15	127	3	218.746493	195.863675	-105.727350	7.932919e-12
XEC.9	305	40	217.415245	194.405749	-102.811498	1.842312e-12
XEC.33	169	40	217.217325	192.518706	-99.037413	2.797164e-13
XEC.2.1	265	40	217.060504	190.430079	-94.860158	3.459733e-14
XEC.2.2	273	40	215.821498	203.772860	-121.545721	2.161237e-08
XEC.13	30	40	213.552422	196.566633	-107.133266	1.597494e-11
XEC.8	592	37	211.038611	199.432561	-112.865121	2.817503e-10
XEC.18	165	3	207.347002	183.566030	-81.132060	3.610862e-17
XEC.31	66	40	206.714596	189.797799	-93.595599	1.842625e-14

Target sequence

, 241_C|T, 521_523, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3653_C|T, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
9803_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11908_A|G, 12529_A|G, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13426_C|T, 14408_C|T, 15538_G|A,
15714_C|T, 15756_T|A, 16293_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21057_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G,
22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A,
23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25267_C|T,
25584_C|T, 25658_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C

 Case 72 (XEC): USA/LA-CDC-LC1137035/2025



Target: 5350 samples       Number of changes: 141                                               
BC: KP.2.5 + XEC.14        BC BR: 3-4                    BC BR coord: 678 - 679          
Direction L1: <<           Initial region span: 1-3,5-141 Gap history (edge excluded): 3-5
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 1.80e-138 Rec. model vs L2: 1.66e-17                                           
Flags: Model_2BP_Bad_L1_opp

KP.2.5 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.5	66	3	9.391444	NaN	NaN	NaN	*	*	*
CM.3	22	3	6.639909	6.639909	-7.279818	0.063928	*	*
BQ.1.1.7	1146	4	6.349948	2.677297	0.645407	0.001213	*	*
KP.5	77	3	6.000082	6.000082	-6.000164	0.033709	*	*
BN.1.2.3	117	3	5.653341	5.653341	-5.306682	0.023873	*	*
BQ.1.26	121	3	5.611641	5.611641	-5.223282	0.022823	*	*
BA.5.2.48	267	3	5.234796	5.234796	-4.469593	0.015686	*	*
BF.7.24	444	3	4.319240	4.319240	-2.638479	0.006282	*	*
BQ.1.11	1938	3	3.937737	3.937737	-1.875474	0.004296	*	*
BF.3	355	3	3.844681	3.844681	-1.689363	0.003907	*	*

|||||

XEC.14 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.14	193	5	265.924099	NaN	NaN	NaN	*	*	*
XEK.1	88	17	263.493156	202.362097	-96.724194	5.457781e-24
XEC.2.2	273	17	261.614127	225.577593	-143.155185	6.627259e-14
XEC.31	66	17	261.301202	237.335343	-166.670685	8.442393e-09
XEC.29	135	17	260.860876	230.829310	-153.658620	1.262932e-11
XEC.9	305	17	260.732237	249.719111	-191.438222	2.019309e-03	*
XEC.28	39	17	260.658672	237.593207	-167.186414	1.094919e-08
XEC.19	59	17	260.407751	237.555495	-167.110989	1.051987e-08
XEC.2	921	17	260.352396	220.158678	-132.317356	2.933985e-16
XEC.8	592	5	259.445082	249.445082	-190.890165	1.533811e-03	*	*

Target sequence

, 241_C|T, 592_T|C, 670_T|G, 875_C|A, 897_C|A, 2060_G|A, 2644_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6411_A|G, 6912_A|G, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/MA-MASPHL-13857/2025



Target: 5350 samples       Number of changes: 145                                               
BC: XEC.2 + JN.1.4         BC BR: 134-135                    BC BR coord: 28271 - 28272  
Direction L1: >>           Initial region span: 1-134,135-145 Gap history (edge excluded):
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 6.64e-28 Rec. model vs L2: 1.23e-40                                           
Flags: Model_2BP_Bad_L1_opp

XEC.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	134	239.094108	NaN	NaN	NaN	*	*	*
MC.24.1	25	140	215.448660	208.647334	-133.294669	5.966684e-14
XEC.25	13	134	213.044929	213.044929	-142.089858	4.859916e-12		*
XEC.9	305	134	210.992612	210.992612	-137.985223	6.256408e-13		*
KP.3.3	1715	134	209.495652	209.495652	-134.991304	1.395993e-13		*
KP.2	1589	140	205.753893	199.057093	-114.114186	4.081774e-18
XEC.18	165	134	205.121870	205.121870	-126.243739	1.757296e-15		*
XEC.24	11	134	205.084947	205.084947	-126.169895	1.696855e-15		*
XEC.36	30	134	205.002307	205.002307	-126.004613	1.558582e-15		*
XEC.17	13	134	204.856962	204.856962	-125.713924	1.348208e-15		*

|||||

JN.1.4 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.4	8971	135	8.824759	NaN	NaN	NaN	*	*	*
XBB.1.6	63	143	7.701175	-19.105800	66.211599	7.415751e-13
KP.3.1.1	12013	135	7.486499	7.486499	13.027002	2.618457e-01	*	*
GN.1.2	14	143	6.780777	-20.100305	68.200610	2.741777e-13
FL.21.2	11	143	6.569954	-24.200491	76.400982	4.543858e-15
JN.1.4.5	1757	142	6.358146	3.108803	21.782394	3.296151e-03	*
CB.1	82	143	6.308325	-20.523342	69.046684	1.792491e-13
BA.2.47	679	142	6.044353	-10.777386	49.554773	3.074880e-09
LZ.1.1	18	143	6.026834	-16.469150	60.938301	1.034001e-11
BU.2	67	143	6.016630	-23.834289	75.668578	6.545491e-15

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 679_C|T, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5822_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11546_A|G, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 14514_T|C, 15651_T|C, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21875_A|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22347_C|T, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29212_G|A, 29479_T|C, 29510_A|C, 29670_C|T, 29734_29759

 Case 72 (XEC): USA/MA-MASPHL-13878/2025



Target: 5350 samples        Number of changes: 146                                                                  
BC: XEC.31 + JN.1.1 + XEC.31 BC BR: 10-11, 38-39                   BC BR coord: 3566 - 3567, 15590 - 15591    
Direction L1: <<            Initial region span: 1-10,11-30,39-146 Gap history (edge excluded): 10-39 -> 30-39
Alt. candidates: [], []                                                                                                    
Model 1BP/2BP comparison:   2BP vs 1BP: 1.36e-18                                                                           
Rec. model vs L1: 1.20e-27  Rec. model vs L2: 1.01e-73                                                              
Flags: Model_2BP_Best

XEC.31 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.31	66	10	23.393083	None	None	None	*	*	*

|||||

JN.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.1	3081	30	28.676856	NaN	NaN	NaN	*	*	*
JN.1.13.1	751	36	20.906996	0.906996	68.186008	7.228963e-07
JN.1.8.1	1498	30	19.265047	4.667079	60.665842	3.104726e-05	*	*
MC.10.1	650	30	18.299583	-16.204617	102.409234	2.681004e-14		*
JN.1	17255	36	17.872708	17.404804	35.190392	1.059095e+01	*
JN.1.4	8971	36	17.711033	9.920049	50.159903	5.946217e-03	*
KP.3.1.1	12013	34	16.845862	9.661502	50.676995	4.584840e-03	*
KP.2.2	1334	36	14.772792	-5.227208	80.454417	1.573442e-09
KP.2.3	4440	36	14.513041	4.129563	61.740875	1.818343e-05	*
KV.2	236	15	14.209157	-19.308873	108.617746	1.201747e-15

|||||

XEC.31 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.31	66	39	246.096884	NaN	NaN	NaN	*	*	*
XEC.2.2	273	39	245.650945	253.813632	-267.627264	1.557521e-07		*
XEC.9	305	39	244.700294	268.105049	-296.210099	2.503238e-01	*	*
XEC.18	165	39	238.974479	262.276532	-284.553065	7.354706e-04	*	*
XEC.33	169	32	238.970357	256.022860	-272.045719	1.419792e-06
XEC.39	155	39	238.163561	260.707696	-281.415392	1.537781e-04	*	*
XEC.40	52	43	238.110565	256.875311	-273.750623	3.321812e-06
XEK.1	88	43	237.996332	239.734737	-239.469473	1.195550e-13
XEC.2.1	265	43	237.810630	240.690964	-241.381927	3.106840e-13
XEC.25	13	43	237.720550	254.819385	-269.638770	4.255004e-07

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6353_T|C, 7842_A|G, 8290_C|T, 8293_C|T, 8393_G|A, 8860_C|T,
9344_C|T, 9424_A|G, 9534_C|T, 9967_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12757_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15042_T|C, 15588_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 17502_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/MA-MASPHL-13989/2025



Target: 5350 samples        Number of changes: 149                                                           
BC: XEC.19 + KP.2.3 + XEC.19 BC BR: 9-10, 15-16                   BC BR coord: 3566 - 3567, 6899 - 6900
Direction L1: <<            Initial region span: 1-9,10-15,16-149 Gap history (edge excluded): 9-16 -> 
Alt. candidates: [], []                                                                                             
Model 1BP/2BP comparison:   2BP vs 1BP: 4.96e-14                                                                    
Rec. model vs L1: 3.43e-20  Rec. model vs L2: 8.02e-82                                                       
Flags: Model_2BP_Best

XEC.19 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.19	59	9	19.453239	None	None	None	*	*	*

|||||

KP.2.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3	4440	15	8.729715	NaN	NaN	NaN	*	*	*
MC.36	49	12	8.538252	-7.851957	41.703915	6.300826e-08
LU.2.1.1	49	12	8.538252	-14.304510	54.609019	9.908927e-11
XBB.1.5.86	101	12	7.814951	-22.185049	70.370097	3.747884e-14
FL.13	151	12	7.399459	-35.879717	97.759433	4.227885e-20
XBB.2.3	695	11	6.202173	-35.285736	96.571472	7.665286e-20
BA.1.21.1	65	10	6.108827	-48.037197	122.074395	2.224712e-25
KP.3.1.1	12013	14	5.992641	5.502703	14.994593	3.975578e-02	*	*
BA.5.1.2	2225	12	5.408043	-17.996531	61.993061	2.474457e-12
EG.5.1.4	1717	12	4.978238	-29.441046	84.882091	2.648376e-17

|||||

XEC.19 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.19	59	16	215.078272	NaN	NaN	NaN	*	*	*
XEC.29	135	16	212.613878	233.603918	-159.207835	3.965314e-01	*	*
XEC.2	921	14	210.878415	212.337568	-116.675136	2.306776e-10
XEC.14	193	16	208.923291	229.599654	-151.199308	7.226503e-03	*	*
XEC.8	592	1	205.591952	219.268660	-130.537320	2.358665e-07
XEC.40	52	16	205.362088	225.966571	-143.933143	1.906636e-04	*	*
XEC.39	155	16	203.865924	224.225056	-140.450111	3.346535e-05	*	*
KP.3.1.1	12013	1	202.976380	197.473676	-86.947352	8.076403e-17
XEC.9	305	1	200.893179	213.908285	-119.816570	1.108786e-09
KP.3.3	1715	16	199.390583	211.340453	-114.680905	8.486155e-11		*

Target sequence

, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3754_A|G, 4184_G|A, 4321_C|T, 5175_C|T, 6183_A|G, 6896_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10456_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13043_G|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19875_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23262_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25234_G|A, 25429_G|T,
25584_C|T, 25703_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27630_C|A, 27807_C|T,
27810_T|C, 28254, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/MI-MDHHS-SC45757/2025



Target: 5350 samples      Number of changes: 142                                                   
BC: KP.3.1.1 + XEC.19     BC BR: 14-15                    BC BR coord: 6183 - 6184          
Direction L1: <<          Initial region span: 1-14,16-142 Gap history (edge excluded): 14-16
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 3.57e-01                                                            
Rec. model vs L1: 1.86e-73 Rec. model vs L2: 2.83e-16                                               
Flags: Model_1BP_Best

KP.3.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.1	12013	14	14.895823	NaN	NaN	NaN	*	*	*
XEC.18	165	12	13.579186	7.188977	19.622046	4.505687e-04	*
JN.1.42.1	18	4	10.232834	-14.057470	62.114939	2.674082e-13
JN.1.61	13	4	9.516802	-6.489302	46.978605	5.159558e-10
BA.2.86.2	74	4	8.876299	-34.321045	102.642090	4.228605e-22
KP.3.1	1957	14	8.727667	8.727667	16.544667	2.101718e-03	*	*
JN.1.67	32	4	8.616016	-7.310046	48.620093	2.272433e-10
JN.1.18.3	97	4	7.507040	-8.527824	51.055648	6.708907e-11
PP.1	127	4	7.172964	-21.065694	76.131387	2.414184e-16
JN.1.7.5	427	4	7.064239	1.991836	30.016329	2.485591e-06

|||||

XEC.19 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.19	59	16	260.283476	NaN	NaN	NaN	*	*	*
XEC.4	192	6	255.079262	244.761483	-221.522966	3.985869e-03	*
XEC.14.1	14	6	253.984259	243.623920	-219.247840	1.281146e-03	*
XEC.31	66	16	247.089186	237.089186	-206.178373	1.859877e-06		*
XEC.29	135	16	246.648860	228.085783	-188.171565	2.283823e-10		*
XEC.9	305	16	246.520222	230.437406	-192.874813	2.394719e-09		*
XEC.14	193	6	246.502684	236.158011	-204.316021	7.338215e-07
XEC.28	39	16	246.446656	236.446656	-204.893313	9.758080e-07		*
XEC.2	921	16	246.133855	236.133855	-204.267710	7.157034e-07		*
XEC.17	13	6	245.520726	235.160386	-202.320773	2.699579e-07

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1347_C|T, 1549_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4927_C|T, 6183_A|G, 6912_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19170_C|A, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A,
22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G,
26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27600_C|T, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29046_C|T, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/MI-UM-10063263439/2025



Target: 5350 samples      Number of changes: 151                                                   
BC: XEC.8 + XEC.2         BC BR: 13-14                    BC BR coord: 6183 - 6184          
Direction L1: <<          Initial region span: 1-11,16-151 Gap history (edge excluded): 11-16
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 5.83e-03                                                            
Rec. model vs L1: 3.82e-31 Rec. model vs L2: 1.29e-12                                               
Flags: Model_1BP_Best

XEC.8 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.8	592	11	26.139423	NaN	NaN	NaN	*	*	*
KP.3.3	1715	13	20.929997	20.929997	-15.859993	3.254374e+00	*
XEC.18	165	14	20.707592	17.110728	-8.221456	7.136127e-02	*
XEC.33	169	14	20.642463	17.045455	-8.090910	6.687032e-02	*
MC.24	831	13	19.806993	19.806993	-13.613986	1.056541e+00	*
KP.3.1.1	12013	13	16.574239	16.574239	-7.148477	4.179410e-02	*
XEC.9	305	13	16.449763	16.449763	-6.899526	3.688317e-02	*
XEC.16	23	15	13.603314	5.079158	15.841683	4.255004e-07
JN.1.8.1	1498	14	11.990692	8.388417	9.223166	1.165238e-05	*
JN.1	17255	14	11.476711	7.874986	10.250028	6.962305e-06

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	16	246.921343	NaN	NaN	NaN	*	*	*
XEC.8	592	1	201.070379	181.321165	-62.642329	1.939078e-26
XEC.2.2	273	13	200.028422	196.418630	-92.837261	7.005544e-20
KP.3.1.1	12013	1	195.448802	178.874563	-57.749127	1.681687e-27
XEC.18	165	5	187.838093	165.434026	-30.868053	2.448090e-33
XEC.40	52	16	184.390794	177.993737	-55.987475	6.975351e-28		*
KP.3.3	1715	1	179.631975	158.701979	-17.403957	2.909739e-36
JN.1	17255	6	178.389892	164.989949	-29.979898	1.568795e-33
XEC.29	135	16	178.007347	163.047212	-26.094425	2.243177e-34		*
XEC.9	305	5	174.577957	152.810670	-5.621341	8.051180e-39

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1387_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4754_C|T, 6183_A|G, 7842_A|G, 8074_C|T, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10702_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13968_C|T, 14408_C|T, 15540_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19728_T|C, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22224_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22599_G|T, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G,
22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A,
23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
25668_A|G, 26058_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26832_G|T, 26833_C|T, 26858_C|T, 27084_G|T, 27107_A|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29499_A|T, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/MN-MDH-46757/2025



Target: 5350 samples      Number of changes: 147                                                            
BC: XEC.32 + BR.3 + XEC.32 BC BR: 5-6, 9-10                   BC BR coord: 2060 - 2061, 3430 - 3431   
Direction L1: <<          Initial region span: 1-3,6-9,10-147 Gap history (edge excluded): 3-10 -> 3-6
Alt. candidates: [], []                                                                                            
Model 1BP/2BP comparison: 2BP vs 1BP: 6.19e-07                                                                     
Rec. model vs L1: 6.38e-15 Rec. model vs L2: 0.00e+00                                                        
Flags: Model_2BP_Best

XEC.32 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.32	42	3	4.718819	None	None	None	*	*	*

|||||

BR.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
BR.3	23	6	9.952023	NaN	NaN	NaN	*	*	*
B.1.568	466	7	8.694898	-1.305102	12.610205	1.294242e-05	*	*
GS.1	109	6	8.676527	8.676527	-7.353054	2.794310e-01	*	*
XBB.1.5.52	654	6	8.080372	8.080372	-6.160744	1.541237e-01	*	*
GJ.3	25	8	6.941899	-1.980893	13.961786	6.589718e-06
BA.4.1.2	19	8	6.941899	-1.980893	13.961786	6.589718e-06
XBB.1.3	10	8	5.737926	-3.184866	16.369732	1.974886e-06
LP.8.1	1124	6	5.683011	5.683011	-1.366022	1.405187e-02	*	*
B.1.36.9	152	8	5.009061	-22.064144	54.128289	1.247562e-14
XBB.1.5.59	284	6	4.969515	4.969515	0.060970	6.874063e-03	*	*

|||||

XEC.32 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.32	42	10	230.184908	NaN	NaN	NaN	*	*	*
XEC.8	592	8	225.447391	224.204075	-138.408150	9.256633e-04	*
XEC.9	305	10	224.875219	225.844096	-141.688192	4.771951e-03	*	*
XEC.2	921	8	222.287797	206.852916	-103.705832	2.700498e-11
XEC.18	165	10	217.703982	218.690965	-127.381929	3.726653e-06		*
KP.3.3	1715	8	216.503013	220.881331	-131.762663	3.329844e-05	*
XEC.14	193	10	210.716170	211.695253	-113.390506	3.415302e-09		*
XEC.29	135	15	210.702025	210.680829	-111.361658	1.237714e-09
XEC.17	13	10	209.734212	210.739433	-111.478865	1.314250e-09		*
XEC.15	127	10	207.439707	208.429054	-106.858108	1.304541e-10		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1513_C|T, 2060_G|A, 2790_C|T, 2918_C|T, 3037_C|T, 3176_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12436_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13711_A|G, 14408_C|T, 15714_C|T, 15756_T|A,
16323_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22329_C|T, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23896_C|T, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
25766_T|C, 26060_C|T, 26270_C|T, 26510_T|C, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/MT-MTPHL-4166796/2025



Target: 5350 samples       Number of changes: 141                                           
BC: XEC.4.6 + XEC.2        BC BR: 3-4                    BC BR coord: 2060 - 2061    
Direction L1: <<           Initial region span: 1-3,4-141 Gap history (edge excluded):
Alt. candidates: [], []                                                                            
Model 1BP/2BP comparison:  -                                                                       
Rec. model vs L1: 1.84e-42 Rec. model vs L2: 3.74e-09                                       
Flags: Model_2BP_Bad_L1_opp

XEC.4.6 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4.6	10	3	7.272505	NaN	NaN	NaN	*	*	*
XEC.4.6.1	13	3	3.917565	3.917565	0.164870	0.034909	*	*
XEC.19	59	3	3.802697	3.802697	0.394607	0.031117	*	*
XEC.28	39	3	3.777179	3.777179	0.445642	0.030197	*	*
XEC.6	45	3	3.772984	3.772984	0.454033	0.030197	*	*
XEC.15	127	3	3.766384	3.766384	0.467232	0.029897	*	*
XEC.4	192	3	3.766259	3.766259	0.467482	0.029897	*	*
XEC.4.1	68	3	3.765326	3.765326	0.469348	0.029897	*	*
XEC.33	169	3	3.762595	3.762595	0.474811	0.029897	*	*
XEC.8	592	3	3.756099	3.756099	0.487802	0.029599	*	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	4	244.566822	NaN	NaN	NaN	*	*	*
KP.3.3	1715	3	222.915227	221.185623	-142.371245	7.017703e-11		*
XEC.8	592	3	222.902776	216.628270	-133.256540	7.378764e-13		*
XEC.14	193	3	221.147457	214.861056	-129.722113	1.256847e-13		*
XEC.19	59	3	219.947967	213.661566	-127.323132	3.785550e-14		*
XEC.4	192	3	216.365937	210.079536	-120.159071	1.055249e-15		*
XEC.9	305	3	215.046790	208.760389	-117.520779	2.818942e-16		*
XEC.33	169	3	214.779127	208.498660	-116.997320	2.173549e-16		*
XEC.13	30	3	213.989807	207.703405	-115.406811	9.815341e-17		*
XEC.39	155	3	213.666943	207.387014	-114.774029	7.127400e-17		*

Target sequence

, 241_C|T, 670_T|G, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T,
10323_A|G, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15177_A|T, 15714_C|T, 15756_T|A, 17410_C|T, 18131_C|T, 18163_A|G,
18395_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21774_C|T, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22624_C|T, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24865_C|T, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25139_T|C, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C

 Case 72 (XEC): USA/NC-CDC-LC1136794/2025



Target: 5350 samples       Number of changes: 142                                                   
BC: MC.24 + XEC.2          BC BR: 13-14                    BC BR coord: 6183 - 6184          
Direction L1: <<           Initial region span: 1-13,15-142 Gap history (edge excluded): 13-15
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 3.82e-118 Rec. model vs L2: 5.39e-21                                               
Flags: Model_2BP_Bad_L1_opp

MC.24 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.24	831	13	12.224416	NaN	NaN	NaN	*	*	*
MC.6	366	4	9.223728	-3.937710	43.875419	9.541787e-08
CQ.1	92	3	7.678656	-59.033676	154.067351	1.127652e-31
BQ.1.1.67	297	3	6.510885	-63.994790	163.989580	7.908144e-34
BQ.1.1.5	1362	3	5.676021	-51.796692	139.593384	1.572053e-28
KS.1.3	45	13	5.226691	5.226691	25.546617	9.118820e-04	*	*
XEC.25	13	13	5.079158	5.079158	25.841683	7.887982e-04	*	*
XEC.18.3	13	13	5.079158	5.079158	25.841683	7.887982e-04	*	*
XEC.32	42	13	5.079158	5.079158	25.841683	7.887982e-04	*	*
XEC.22	23	13	5.079158	5.079158	25.841683	7.887982e-04	*	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	15	265.162474	NaN	NaN	NaN	*	*	*
XEC.36	30	4	259.769990	245.816197	-217.632395	8.740134e-05	*
XEC.38	34	4	259.579917	245.652848	-217.305695	7.447850e-05	*
XEC.29	135	15	259.430411	240.867333	-207.734667	6.190994e-07		*
XEC.31	66	15	258.976919	248.976919	-223.953839	2.060102e-03	*	*
XEC.32	42	4	258.937850	244.950156	-215.900312	3.680047e-05	*
XEC.13	30	4	258.227125	244.273333	-214.546666	1.873719e-05	*
XEK.1	88	22	258.080150	239.567712	-205.135423	1.695700e-07
XEK.5	28	22	257.040926	238.528488	-203.056975	5.993531e-08
XEC.9	305	15	256.877298	240.794482	-207.588965	5.772445e-07		*

Target sequence

, 241_C|T, 670_T|G, 885_G|T, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3246_G|A, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7480_T|C, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 9693_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16887_C|T,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18743_A|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/CA-LACPHL-AY12004/2025



Target: 5350 samples       Number of changes: 141                                               
BC: KP.2.5 + XEC.14        BC BR: 3-4                    BC BR coord: 678 - 679          
Direction L1: <<           Initial region span: 1-3,5-141 Gap history (edge excluded): 3-5
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 7.13e-145 Rec. model vs L2: 1.66e-17                                           
Flags: Model_2BP_Bad_L1_opp

KP.2.5 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.5	66	3	9.391444	NaN	NaN	NaN	*	*	*
CM.3	22	3	6.639909	6.639909	-7.279818	0.063928	*	*
BQ.1.1.7	1146	4	6.349948	2.677297	0.645407	0.001213	*	*
KP.5	77	3	6.000082	6.000082	-6.000164	0.033709	*	*
BN.1.2.3	117	3	5.653341	5.653341	-5.306682	0.023873	*	*
BQ.1.26	121	3	5.611641	5.611641	-5.223282	0.022823	*	*
BA.5.2.48	267	3	5.234796	5.234796	-4.469593	0.015686	*	*
BF.7.24	444	3	4.319240	4.319240	-2.638479	0.006282	*	*
BQ.1.11	1938	3	3.937737	3.937737	-1.875474	0.004296	*	*
BF.3	355	3	3.844681	3.844681	-1.689363	0.003907	*	*

|||||

XEC.14 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.14	193	5	276.499648	NaN	NaN	NaN	*	*	*
XEC.8	592	5	271.990858	261.990858	-225.981716	1.099846e-02	*	*
XEC.9	305	5	269.837039	259.837039	-221.674078	1.274757e-03	*	*
XEC.3	29	8	264.226759	254.140514	-210.281029	4.286672e-06
XEC.13	30	8	262.691703	252.605458	-207.210917	9.235878e-07
XEC.29	135	16	261.793841	241.762275	-185.524550	1.801169e-11
XEC.2	921	16	261.562400	231.368682	-164.737365	5.536494e-16
XEC.18	165	8	259.889050	249.790648	-201.581295	5.532727e-08
XEC.33	169	8	257.721668	247.605535	-197.211071	6.223085e-09
XEC.30	135	8	256.872574	246.748818	-195.497635	2.646574e-09

Target sequence

 Case 72 (XEC): USA/NMDOH-2025013208/2025



Target: 5350 samples       Number of changes: 145                                                   
BC: KP.3.1.1 + XEC.27      BC BR: 15-16                    BC BR coord: 7367 - 7368          
Direction L1: <<           Initial region span: 1-12,16-145 Gap history (edge excluded): 12-16
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 5.14e-55 Rec. model vs L2: 2.03e-08                                               
Flags: Model_2BP_Bad_L1_opp

KP.3.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.1	12013	12	12.481728	NaN	NaN	NaN	*	*	*
XEC.19	59	11	12.093654	-21.084319	92.168638	1.210073e-08		*
JN.1.8.1	1498	12	7.534864	-11.976290	73.952579	1.094547e-04	*	*
PD.2.1	10	3	7.171233	-51.357525	152.715049	8.600945e-22
XEC.32	42	14	6.995760	-3.004240	56.008481	8.607080e-01	*
KP.2.2	1334	12	6.656877	-12.688307	75.376614	5.354436e-05	*	*
JN.1.7.8	34	3	5.902722	-36.516483	123.032967	2.407952e-15
JN.1.11	43	3	5.583160	-30.464071	110.928141	1.021244e-12
BQ.1.1.18	1989	4	5.425645	-45.601394	141.202788	2.729495e-19
JN.1	17255	12	4.574337	0.945412	48.109176	4.470118e+01	*	*

|||||

XEC.27 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.27	25	16	211.414459	NaN	NaN	NaN	*	*	*
XEC.2	921	16	203.967771	203.967771	-125.935542	5.843561e-04	*	*
XEC.32	42	5	203.021342	183.489692	-84.979384	7.452922e-13
XEK.5	28	16	201.087826	201.087826	-120.175651	3.280269e-05	*	*
KP.3.3	1715	15	197.635552	196.601549	-111.203097	3.680673e-07		*
XEC.15	127	16	194.812415	194.812415	-107.624830	6.145258e-08		*
XEC.29	135	16	194.314388	194.314388	-106.628776	3.745971e-08		*
XEC.9	305	16	194.082834	194.082834	-106.165668	2.976299e-08		*
XEC.14	193	16	193.474180	193.474180	-104.948361	1.617175e-08		*
XEC.31	66	16	189.834481	189.834481	-97.668962	4.245463e-10		*

Target sequence

, 241_C|T, 670_T|G, 897_C|G, 1148_G|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6362_G|A, 7318_C|T, 7360_G|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15162_A|G, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18186_G|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22893_A|C, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25324_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28851_G|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29134_G|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/NY-CDC-LC1135259/2025



Target: 5350 samples      Number of changes: 147                                                               
BC: KP.3.3 + KS.1 + KP.3.3 BC BR: 6-7, 16-17                   BC BR coord: 2060 - 2061, 7118 - 7119     
Direction L1: <<          Initial region span: 1-6,7-15,17-147 Gap history (edge excluded): 6-17 -> 15-17
Alt. candidates: [], []                                                                                               
Model 1BP/2BP comparison: 2BP vs 1BP: 1.07e-02                                                                        
Rec. model vs L1: 1.23e-21 Rec. model vs L2: 4.75e-90                                                           
Flags: Model_2BP_Best

KP.3.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.3	1715	6	7.681506	None	None	None	*	*	*

|||||

KS.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KS.1	505	15	19.327580	NaN	NaN	NaN	*	*	*
KP.3.1.1	12013	16	15.830678	11.444617	19.110766	8.289586e+00	*	*
MC.19	221	11	14.033159	-4.597003	51.194006	8.962916e-07
XEC.11.1	166	11	12.714431	-19.879797	81.759593	2.061855e-13
JN.1.32	436	11	11.706616	-2.545936	47.091871	6.962305e-06
MC.10.1	650	11	11.319780	-7.311921	56.623843	5.933895e-08
XEK.1	88	10	9.687591	-29.726620	101.453240	1.093022e-17
JN.1	17255	11	9.428992	-4.824643	51.649287	7.121338e-07
JN.3	321	10	8.393487	-22.187899	86.375797	2.046623e-14
BL.1.3	10	9	8.287639	-60.142726	162.285453	6.720334e-31

|||||

KP.3.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.3	1715	17	240.659483	NaN	NaN	NaN	*	*	*
XEC.14	193	13	238.986499	231.297759	-174.595518	3.977608e-08
XEC.6	45	13	235.908261	214.763895	-141.527791	2.621578e-15
XEC.33	169	32	226.386729	224.576511	-161.153022	4.775201e-11
XEC.2.1	265	32	226.166983	194.579219	-101.158437	4.490851e-24
XEC.8	592	17	220.315464	220.758603	-153.517207	1.052345e-12		*
XEK.6	23	24	219.180173	189.773365	-91.546730	3.677424e-26
XEC.31	66	17	218.670168	209.644854	-131.289707	1.566661e-17		*
XEC.29	135	17	218.229842	209.235063	-130.470125	1.039715e-17		*
XEC.9	305	17	218.101204	209.070081	-130.140163	8.815678e-18		*

Target sequence

, 241_C|T, 337_C|T, 556_C|T, 670_T|G, 897_C|A, 2060_G|A, 2526_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4113_C|T, 4184_G|A, 4321_C|T, 6183_A|G, 6218_T|C, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 9923_G|A, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12053_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21897_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24912_C|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25460_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28153_C|T,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/NY-CDC-LC1136530/2025



Target: 5350 samples       Number of changes: 144                                           
BC: BQ.1.1.7 + XEC.8       BC BR: 5-6                    BC BR coord: 874 - 875      
Direction L1: <<           Initial region span: 1-5,6-144 Gap history (edge excluded):
Alt. candidates: [], []                                                                            
Model 1BP/2BP comparison:  -                                                                       
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 2.51e-18                                       
Flags: Model_2BP_Bad_L1_opp

BQ.1.1.7 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
BQ.1.1.7	1146	5	7.593118	NaN	NaN	NaN	*	*	*
BF.7.24	444	4	5.257856	-4.742144	23.484288	4.395189e-06		*
BQ.1.11	1938	4	4.655529	-5.344471	24.688942	2.400100e-06		*
JN.1.22	516	4	4.257580	-5.742420	25.484840	1.616900e-06		*
BA.2.86.1	1343	4	4.060345	-5.939655	25.879310	1.323806e-06		*
AY.43.9	285	3	3.744530	-16.255470	46.510940	4.386081e-11
XBB.1.5.21	611	4	3.730621	-6.269379	26.538758	9.517152e-07		*
XFG.3	480	4	3.720497	-6.279503	26.559005	9.422455e-07		*
BQ.1	15159	4	3.542165	-6.457835	26.915670	7.870296e-07		*
BA.2.8	4985	4	2.995111	-7.004889	28.009777	4.563526e-07		*

|||||

XEC.8 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.8	592	6	263.956456	NaN	NaN	NaN	*	*	*
XEC.14	193	6	256.499648	256.499648	-212.999296	5.785417e-04	*	*
XEC.2	921	17	252.616041	232.422324	-164.844647	2.016153e-14
XEC.29	135	18	251.793841	231.762275	-163.524550	1.042051e-14
XEC.9	305	18	250.850166	249.837039	-199.674078	7.374998e-07
XEC.3	29	18	250.187912	244.140514	-188.281029	2.480018e-09
XEC.13	30	18	248.651666	242.605458	-185.210917	5.343340e-10
XEC.30	135	9	248.236963	248.113206	-196.226412	1.320613e-07
XEC.17	13	9	247.151054	247.064810	-194.129620	4.621322e-08
XEC.18	165	18	245.833461	239.790648	-179.581295	3.200913e-11

Target sequence

, 241_C|T, 516_518, 592_T|C, 670_T|G, 875_C|A, 897_C|A, 2060_G|A, 2644_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6912_A|G, 7765_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11020_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25987_G|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/NY-CDC-LC1136873/2025



Target: 5350 samples      Number of changes: 147                                               
BC: XEC.9 + XEC.2         BC BR: 6-7                    BC BR coord: 2060 - 2061        
Direction L1: <<          Initial region span: 1-6,8-147 Gap history (edge excluded): 6-8
Alt. candidates: [], []                                                                               
Model 1BP/2BP comparison: 1BP vs 2BP: 3.68e-01                                                        
Rec. model vs L1: 1.59e+01 Rec. model vs L2: 5.85e-16                                           
Flags: Model_1BP_Best

XEC.9 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.9	305	6	13.156712	NaN	NaN	NaN	*	*	*
MV.1	127	4	10.771135	-9.228865	30.457729	1.898095e-10
MV.2	21	4	10.746124	-9.253876	30.507753	1.851231e-10
MB.1.1.1	53	4	10.634215	-9.365785	30.731570	1.658396e-10
MM.1	35	5	10.514447	0.514447	10.971107	3.239797e-06		*
LF.7.6	15	4	10.389449	-9.610551	31.221103	1.298034e-10
MH.1	51	4	9.400665	-10.599335	33.198670	4.823192e-11
MC.29	54	4	7.904542	-12.095458	36.190916	1.081594e-11
MD.1	19	4	7.850475	-12.149525	36.299050	1.023713e-11
LF.1.1.1	109	4	7.647881	-12.352119	36.704239	8.381452e-12

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	8	239.758565	NaN	NaN	NaN	*	*	*
XEC.8	592	8	237.711377	227.711377	-153.422754	1.287349e-01	*	*
XEC.14	193	8	237.384176	227.384176	-152.768351	9.301449e-02	*	*
XEC.29	135	8	234.072747	224.072747	-146.145495	3.396533e-03	*	*
XEC.32	42	8	231.497436	221.497436	-140.994873	2.573689e-04	*	*
XEC.9	305	1	231.383122	218.226410	-134.452820	9.781673e-06
XEC.31	66	8	230.316550	220.316550	-138.633101	7.908400e-05	*	*
XEC.6	45	8	228.154591	218.154591	-134.309181	9.120372e-06		*
XEC.25	13	5	225.912519	214.233238	-126.466476	1.809582e-07
XEC.30	135	8	224.898591	214.898591	-127.797182	3.518714e-07		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 936_C|T, 1102_C|T, 2060_G|A, 2177_G|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15219_A|G, 15360_C|T, 15714_C|T, 15756_T|A,
16887_C|T, 17410_C|T, 18163_A|G, 18490_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25096_C|T, 25207_C|T, 25584_C|T, 25810_C|T,
26060_C|T, 26093_A|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27654_C|T, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/NY-NYCPHL-019769/2025



Target: 5350 samples       Number of changes: 140                                               
BC: BA.5.1.30 + XEC.2      BC BR: 4-5                    BC BR coord: 672 - 673          
Direction L1: <<           Initial region span: 1-4,7-140 Gap history (edge excluded): 4-7
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 2.60e-10                                           
Flags: Model_2BP_Bad_L1_opp

BA.5.1.30 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
BA.5.1.30	4775	4	2.782144	NaN	NaN	NaN	*	*	*
B.1.243	5209	3	2.218682	-7.781318	23.562636	0.000026	*	*
B.1.258	3961	3	2.077191	-7.922809	23.845617	0.000022	*	*
BA.2	443141	4	1.613450	1.613450	4.773100	0.311923	*	*
BA.2.9	75328	4	1.443566	1.443566	5.112868	0.263158	*	*
BA.5.6	14873	4	1.204625	1.204625	5.590750	0.207008	*	*
BA.5.1	53705	4	0.653552	0.653552	6.692895	0.119433	*	*
BQ.1.1	36940	4	0.483196	0.483196	7.033608	0.100761	*	*
B.1.1.7	477665	3	0.192926	-9.807074	27.614149	0.000003		*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	7	283.039884	NaN	NaN	NaN	*	*	*
XEC.33	169	4	261.294403	260.213439	-222.426878	7.284004e-08
XEC.8	592	4	260.304259	259.243025	-220.486050	2.761242e-08
KP.3.3	1715	4	260.291054	259.214706	-220.429413	2.679635e-08
XEC.39	155	4	259.526352	258.445925	-218.891851	1.240706e-08
XEC.2.1	265	15	258.853734	248.663436	-199.326872	7.018898e-13
XEC.14	193	5	255.648685	247.805866	-197.611733	2.970131e-13
XEC.4	192	4	251.954063	250.867164	-203.734328	6.334565e-12
XEC.38	34	4	251.845531	250.788486	-203.576971	5.876851e-12
XEC.17	13	4	251.298389	250.211491	-202.422981	3.290439e-12

Target sequence

, 241_C|T, 508_T|C, 642_A|G, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6941_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G,
18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21777_G|A, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T,
26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C,
29733_29758, 29759_G|T

 Case 72 (XEC): USA/NY-PRL-250318_81E02/2025



Target: 5350 samples      Number of changes: 142                                                   
BC: XEC.18.3 + XEC.2      BC BR: 12-13                    BC BR coord: 6183 - 6184          
Direction L1: <<          Initial region span: 1-12,14-142 Gap history (edge excluded): 12-14
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 4.70e-01                                                            
Rec. model vs L1: 2.18e-46 Rec. model vs L2: 1.05e-17                                               
Flags: Model_1BP_Best

XEC.18.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.18.3	13	12	15.079158	NaN	NaN	NaN	*	*	*
XEC.22	23	12	15.079158	15.079158	-6.158317	1.000000	*	*
XEC.24	11	12	15.079158	15.079158	-6.158317	1.000000	*	*
XEC.25	13	12	15.079158	15.079158	-6.158317	1.000000	*	*
XEC.4.3	10	12	15.079158	15.079158	-6.158317	1.000000	*	*
XEC.16	23	12	15.079158	15.079158	-6.158317	1.000000	*	*
XEC.17	13	12	15.079158	15.079158	-6.158317	1.000000	*	*
XEC.32	42	12	15.079158	15.079158	-6.158317	1.000000	*	*
XEC.4.1	68	12	15.049528	15.049528	-6.099057	0.970446	*	*
XEC.13	30	12	15.045257	15.045257	-6.090514	0.965605	*	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	14	242.784986	NaN	NaN	NaN	*	*	*
XEC.6	45	5	238.591404	218.322530	-156.645061	5.249305e-07
XEC.9	305	5	238.395407	218.081910	-156.163820	4.108655e-07
XEC.8	592	5	238.391667	218.084474	-156.168948	4.129249e-07
KP.3.3	1715	5	237.583410	221.818211	-163.636423	1.729661e-05	*
XEC.30	135	5	236.488199	216.226930	-152.453861	6.428111e-08
XEC.39	155	5	234.839354	214.524750	-149.049500	1.174310e-08
XEC.14	193	5	234.451604	214.106931	-148.213862	7.715767e-09
XEC.33	169	5	234.450387	214.138066	-148.276132	7.990600e-09
XEC.38	34	5	229.679604	209.379889	-138.759778	6.844436e-11

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1117_T|C, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6547_T|C, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G,
18555_C|T, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21599_21610, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21969_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25855_G|C, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G,
26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C,
28884_G|C, 28958_C|A, 29353_C|T, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/NY-PRL-250318_81E03/2025



Target: 5350 samples       Number of changes: 140                                           
BC: XBC.1.3.1 + XEC.14     BC BR: 4-5                    BC BR coord: 686 - 687      
Direction L1: <<           Initial region span: 1-4,5-140 Gap history (edge excluded):
Alt. candidates: [], []                                                                            
Model 1BP/2BP comparison:  -                                                                       
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 9.94e-20                                       
Flags: Model_2BP_Bad_L1_opp

XBC.1.3.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XBC.1.3.1	13	4	9.312302	NaN	NaN	NaN	*	*	*
BA.4.1.11	107	4	8.829163	8.829163	-9.658327	0.618783	*	*
NL.2.1	16	4	7.653830	7.653830	-7.307660	0.191092	*	*
BA.4.8	14	4	7.084645	7.084645	-6.169289	0.108067	*	*
BA.4.1.9	194	4	6.927847	6.927847	-5.855694	0.092551	*	*
DC.1	59	4	6.801790	6.801790	-5.603581	0.081268	*	*
BA.4.6.1	399	4	5.960023	5.960023	-3.920046	0.035084	*	*
NL.2	237	4	5.913637	5.913637	-3.827273	0.033541	*	*
NL.15	13	3	5.881306	-4.118694	16.237388	0.000001		*
NL.14	12	3	5.881306	-4.118694	16.237388	0.000001		*

|||||

XEC.14 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.14	193	5	280.259967	NaN	NaN	NaN	*	*	*
XEC.9	305	1	274.632388	273.404643	-254.809286	1.054172e-03	*
XEC.30	135	5	271.506529	271.506529	-251.013059	1.576710e-04	*	*
XEC.33	169	3	268.403155	267.842439	-243.684878	4.037035e-06
XEC.38	34	3	264.754147	263.306958	-234.613916	4.330490e-08
XEC.4	192	1	263.872900	263.203786	-234.407573	3.918390e-08
XEC.19	59	1	263.209301	261.566566	-231.133132	7.600894e-09
XEC.17	13	5	262.851212	262.851212	-233.702425	2.747471e-08		*
XEC.16	23	1	261.776075	258.249253	-224.498507	2.761712e-10
XEC.25	13	3	261.125888	257.994287	-223.988574	2.140097e-10

Target sequence

, 241_C|T, 509_523, 670_T|G, 686_694, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5806_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15026_C|T, 15714_C|T, 15756_T|A, 17078_A|G,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T,
22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A,
23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A,
29510_A|C, 29734_29759

 Case 72 (XEC): USA/NY-PRL-250325_82H02/2025



Target: 5350 samples      Number of changes: 141                                                          
BC: XEC.2 + XEC.25 + XEC.2 BC BR: 4-5, 6-7                   BC BR coord: 941 - 942, 2789 - 2790    
Direction L1: <<          Initial region span: 1-3,5-6,7-141 Gap history (edge excluded): 3-7 -> 3-5
Alt. candidates: [], []                                                                                          
Model 1BP/2BP comparison: 2BP vs 1BP: 8.59e-02                                                                   
Rec. model vs L1: 5.00e-17 Rec. model vs L2: 5.21e-25                                                      
Flags: Model_2BP_Best

XEC.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	3	4.681558	None	None	None	*	*	*

|||||

XEC.25 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.25	13	5	11.679280	NaN	NaN	NaN	*	*	*
XEC.9	305	4	8.474236	7.425306	-10.850612	1.419309e-02	*	*
XEC.4	192	5	7.888122	7.888122	-11.776244	2.259560e-02	*	*
XEC.8	592	5	7.443363	7.443363	-10.886727	1.447981e-02	*	*
XEC.18.3	13	6	6.286401	-3.713599	11.427198	2.060803e-07		*
XEC.28	39	6	6.286401	-3.713599	11.427198	2.060803e-07		*
XEC.4.1.4	23	6	6.286401	-3.713599	11.427198	2.060803e-07		*
XEC.4.1	68	6	6.286401	-3.713599	11.427198	2.060803e-07		*
XEC.38	34	6	6.286401	-3.713599	11.427198	2.060803e-07		*
XEC.36	30	6	6.286401	-3.713599	11.427198	2.060803e-07		*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	7	222.193476	NaN	NaN	NaN	*	*	*
XEC.9	305	1	220.891895	213.466589	-114.933178	3.175644e-06
XEC.8	592	5	215.678685	202.885329	-93.770658	8.072280e-11
XEC.31	66	6	213.915344	202.317227	-92.634454	4.565080e-11		*
XEC.14	193	6	213.879702	213.099387	-114.198774	2.204522e-06		*
KP.3.3	1715	1	213.087069	211.945417	-111.890834	6.945512e-07
XEC.15	127	6	210.046975	198.463519	-84.927039	9.714370e-13		*
XEC.6	45	6	204.645884	193.055830	-74.111659	4.343917e-15		*
XEC.32	42	6	203.927310	192.359728	-72.719457	2.167938e-15		*
XEC.30	135	6	202.522072	190.962207	-69.924413	5.346069e-16		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 936_C|T, 1102_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15219_A|G, 15360_C|T, 15714_C|T, 15756_T|A, 16887_C|T,
17410_C|T, 18163_A|G, 18490_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21610_T|C, 21641_G|T, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994,
22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A,
22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25810_C|T, 26060_C|T, 26093_A|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27654_C|T, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/NY-PRL-250401_82H04/2025



Target: 5350 samples       Number of changes: 140                                                            
BC: XEC.2 + B.1.561 + XEC.2 BC BR: 10-11, 13-14                   BC BR coord: 4330 - 4331, 6182 - 6183
Direction L1: <<           Initial region span: 1-10,11-13,14-140 Gap history (edge excluded): 10-14 ->
Alt. candidates: [], []                                                                                             
Model 1BP/2BP comparison:  2BP vs 1BP: 4.98e-06                                                                     
Rec. model vs L1: 9.48e-25 Rec. model vs L2: 0.00e+00                                                        
Flags: Model_2BP_Best

XEC.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	10	5.098043	None	None	None	*	*	*

|||||

B.1.561 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
B.1.561	1058	11	10.280817	NaN	NaN	NaN	*	*	*
AY.94	218	13	6.229347	-13.770653	37.541307	3.591019e-11
B.1.558	181	12	5.536276	-4.463724	18.927449	3.947552e-07		*
FY.1	23	13	5.220251	-14.779749	39.559498	1.307917e-11
B.1.1.50	79	13	5.084910	-24.133193	58.266385	1.131763e-15
AY.20	12743	11	3.657758	3.657758	2.684485	1.333431e-03	*	*
MK.1	151	13	3.338465	-16.661535	43.323069	1.995752e-12
LP.8.1.1	2345	13	2.792929	-4.310545	18.621089	4.609391e-07
BQ.1.8	1899	12	1.751395	0.624919	8.750162	6.410424e-05	*	*
AY.4.6	9691	13	1.479377	-4.957839	19.915678	2.406313e-07

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	14	270.890862	NaN	NaN	NaN	*	*	*
XEC.30	135	1	265.285409	284.461224	-278.922448	4.769515e+03	*
XEC.39	155	14	262.790929	284.208089	-278.416178	3.714502e+03	*	*
XEC.18	165	14	260.586715	282.019496	-274.038993	4.157150e+02	*	*
XEC.14	193	3	258.524785	279.144285	-268.288570	2.345304e+01	*
XEC.19	59	14	258.028613	279.445795	-268.891589	3.165829e+01	*	*
XEC.29	135	19	255.570629	271.104945	-252.209890	7.559124e-03	*
XEK.5	28	19	255.506468	252.480483	-214.960966	6.162213e-11
XEC.9	305	19	255.471357	273.425111	-256.850222	7.691918e-02	*
XEC.31	66	14	254.695317	276.118882	-262.237763	1.138828e+00	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4456_C|T, 5512_C|T, 5999_A|G, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 8655_C|T, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 18912_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T,
22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A,
23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A,
29510_A|C, 29734_29759

 Case 72 (XEC): USA/NY-PRL-250422_82D10/2025



Target: 5350 samples      Number of changes: 146                                               
BC: XEC.9 + XEC.2         BC BR: 6-7                    BC BR coord: 2060 - 2061        
Direction L1: <<          Initial region span: 1-6,8-146 Gap history (edge excluded): 6-8
Alt. candidates: [], []                                                                               
Model 1BP/2BP comparison: 1BP vs 2BP: 3.68e-01                                                        
Rec. model vs L1: 1.65e+01 Rec. model vs L2: 5.82e-16                                           
Flags: Model_1BP_Best

XEC.9 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.9	305	6	13.156712	NaN	NaN	NaN	*	*	*
MV.1	127	4	10.771135	-9.228865	30.457729	1.898095e-10
MV.2	21	4	10.746124	-9.253876	30.507753	1.851231e-10
MB.1.1.1	53	4	10.634215	-9.365785	30.731570	1.658396e-10
MM.1	35	5	10.514447	0.514447	10.971107	3.239797e-06		*
LF.7.6	15	4	10.389449	-9.610551	31.221103	1.298034e-10
MH.1	51	4	9.400665	-10.599335	33.198670	4.823192e-11
MC.29	54	4	7.904542	-12.095458	36.190916	1.081594e-11
MD.1	19	4	7.850475	-12.149525	36.299050	1.023713e-11
LF.1.1.1	109	4	7.647881	-12.352119	36.704239	8.381452e-12

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	8	236.127429	NaN	NaN	NaN	*	*	*
XEC.8	592	8	234.200121	224.200121	-144.400243	1.458758e-01	*	*
XEC.14	193	8	233.752114	223.752114	-143.504228	9.301449e-02	*	*
XEC.29	135	8	230.454130	220.454130	-136.908259	3.447865e-03	*	*
XEC.9	305	1	227.793871	214.637159	-125.274317	1.023190e-05	*
XEC.6	45	8	224.525821	214.525821	-125.051641	9.166088e-06		*
XEC.32	42	8	223.927888	213.927888	-123.855776	5.055671e-06		*
XEC.31	66	8	222.731908	212.731908	-121.463815	1.522739e-06		*
XEC.30	135	8	221.354081	211.354081	-118.708163	3.850087e-07		*
KP.3.3	1715	8	220.933277	210.933277	-117.866554	2.529687e-07		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 936_C|T, 1102_C|T, 2060_G|A, 2177_G|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15219_A|G, 15360_C|T, 15714_C|T, 15756_T|A,
16887_C|T, 17410_C|T, 18163_A|G, 18490_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25096_C|T, 25207_C|T, 25584_C|T, 25810_C|T, 26060_C|T, 26093_A|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27654_C|T, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/NY-PRL-250506_81E06/2025



Target: 5350 samples      Number of changes: 141                                             
BC: KP.3.3 + XEC.2        BC BR: 14-15                    BC BR coord: 6806 - 6807    
Direction L1: <<          Initial region span: 1-14,15-141 Gap history (edge excluded):
Alt. candidates: [], []                                                                             
Model 1BP/2BP comparison: 1BP vs 2BP: 1.35e-01                                                      
Rec. model vs L1: 6.20e-29 Rec. model vs L2: 3.56e-21                                         
Flags: Model_1BP_Best

KP.3.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.3	1715	14	23.967811	NaN	NaN	NaN	*	*	*
KP.3.1.1	12013	14	16.681795	16.681795	2.636410	6.823281e-04	*	*
XEC.27	25	7	15.661018	-5.004223	46.008446	2.608059e-13
XEC.4.1.4	23	7	15.661018	-16.646216	69.292432	2.296834e-18
XEC.8.1	12	7	15.661018	-5.007853	46.015706	2.595051e-13
XEC.36	30	7	15.661018	-4.954743	45.909486	2.741777e-13
XEC.32	42	7	15.661018	-4.920842	45.841683	2.839438e-13
XEC.13	30	7	15.661018	-4.954743	45.909486	2.741777e-13
XEC.3	29	7	15.661018	-4.955933	45.911866	2.741777e-13
XEC.29	135	7	15.661018	-18.940102	73.880203	2.314322e-19

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	15	275.190515	NaN	NaN	NaN	*	*	*
XEC.14	193	15	269.660996	269.660996	-267.321992	3.965989e-03	*	*
XEC.8	592	15	268.822922	268.822922	-265.645843	1.720741e-03	*	*
XEC.18	165	11	267.325535	258.482620	-244.965240	5.560459e-08
XEC.28	39	15	256.483069	256.483069	-240.966138	7.525264e-09		*
XEC.4.3	10	15	255.318638	245.906523	-219.813046	1.912873e-13		*
XEC.9	305	15	255.087002	249.004187	-226.008373	4.246186e-12		*
KP.3.3	1715	1	253.089716	229.121905	-186.243809	9.818683e-21
XEC.4	192	15	251.816343	251.816343	-231.632687	7.052880e-11		*
XEK.1	88	26	246.667131	241.297117	-210.594235	1.903656e-15

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3433_G|A, 3565_T|C, 3688_C|T, 4184_G|A, 4321_C|T, 6183_A|G, 6794_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10582_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23609_C|T, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/OK-CDC-2-8448976/2025



Target: 5350 samples       Number of changes: 142                                                   
BC: JN.1.38 + XEC.2        BC BR: 13-14                    BC BR coord: 7842 - 7843          
Direction L1: <<           Initial region span: 1-13,15-142 Gap history (edge excluded): 13-15
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  1BP vs 2BP: 7.38e-09                                                            
Rec. model vs L1: 1.34e-112 Rec. model vs L2: 1.40e-21                                               
Flags: Model_1BP_Best

JN.1.38 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.38	247	13	23.844392	NaN	NaN	NaN	*	*	*
JN.1.18	431	13	23.358963	23.358963	-14.717926	6.156972e-01	*	*
JN.1.9	576	13	22.162810	22.162810	-12.325620	1.863740e-01	*	*
JN.1	17255	13	20.813196	20.813196	-9.626392	4.831564e-02	*	*
BA.2.86.1	1343	13	20.598213	20.598213	-9.196426	3.896856e-02	*	*
JN.1.45	268	10	19.003710	16.208954	-0.417907	4.832386e-04	*
MC.13	807	12	18.983062	18.199194	-4.398388	3.535148e-03	*	*
MC.40	21	10	18.817432	11.643355	8.713290	5.030456e-06
XEC.2.6	13	10	18.623899	8.017767	15.964466	1.340571e-07
JN.1.5	174	10	18.432058	13.317145	5.365710	2.672262e-05	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	15	260.483777	NaN	NaN	NaN	*	*	*
XEC.30	135	15	247.270755	237.270755	-202.541510	1.823049e-06		*
XEC.9	305	15	244.297465	234.297465	-196.594929	9.306199e-08		*
XEK.5	28	25	244.139319	229.553173	-187.106347	8.132358e-10
XEC.2.2	273	25	243.474717	227.666603	-183.333206	1.228570e-10
XEC.13	30	15	242.101942	232.101942	-192.203885	1.036325e-08		*
XEC.8	592	15	238.625867	228.625867	-185.251734	3.208652e-10		*
XEC.39	155	15	237.278104	227.278104	-182.556208	8.359813e-11		*
XEC.31	66	5	235.978142	222.891816	-173.783633	1.036678e-12
XEC.29	135	15	233.278671	223.278671	-174.557342	1.531153e-12		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2485_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5672_C|T, 6183_A|G, 7842_A|G, 8157_C|T, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11005_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 15951_C|T, 16887_C|T,
17410_C|T, 18163_A|G, 18395_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20703_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C

 Case 72 (XEC): USA/OK-CDC-2-8506526/2025



Target: 5350 samples      Number of changes: 143                                                   
BC: XEC.15 + XEC.2        BC BR: 13-14                    BC BR coord: 4387 - 4388          
Direction L1: <<          Initial region span: 1-10,14-143 Gap history (edge excluded): 10-14
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 3.47e-07                                                            
Rec. model vs L1: 2.58e-16 Rec. model vs L2: 1.53e-24                                               
Flags: Model_1BP_Best

XEC.15 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.15	127	10	12.064195	NaN	NaN	NaN	*	*	*
XEC.5	126	10	11.428839	3.559696	28.880607	5.220458e-01	*	*
KP.3.1.1	12013	10	11.301197	3.446806	29.106387	4.653339e-01	*	*
MC.9	298	4	9.587999	-9.999051	55.998101	6.740241e-07
MC.13	807	4	9.291477	-10.277047	56.554093	5.119699e-07
MC.11	393	4	9.290290	-10.284216	56.568432	5.068757e-07
LF.4.1	50	3	4.718819	-29.546164	95.092328	2.189726e-15
LB.1.3.3	22	3	4.718819	-24.817034	85.634067	2.480862e-13
LD.1.1	11	3	4.718819	-43.530791	123.061582	1.848338e-21
LD.2	13	3	4.718819	-49.801673	135.603346	3.497478e-24

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	14	249.259018	NaN	NaN	NaN	*	*	*
KP.3.3	1715	8	244.758422	234.888416	-187.776831	5.743654e-07
XEC.8	592	12	244.573331	242.428163	-202.856327	1.080858e-03	*
XEC.33	169	31	243.012472	232.285952	-182.571905	4.244741e-08
XEC.2.1	265	31	242.855651	238.985469	-195.970939	3.448452e-05	*
XEC.14	193	12	240.191495	238.044637	-194.089274	1.347061e-05	*
XEC.13	30	12	236.933225	234.786367	-187.572733	5.171153e-07
XEC.18	165	31	236.889053	233.938277	-185.876554	2.221307e-07
XEC.29	135	15	235.836792	225.449683	-168.899367	4.565080e-11		*
XEC.4	192	12	235.346048	233.199190	-184.398380	1.059816e-07

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1976_G|A, 2060_G|A, 2790_C|T, 2937_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4092_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 9724_C|T, 10029_C|T, 10198_C|T, 10323_A|G, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11967_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24023_C|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25003_A|G, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C

 Case 72 (XEC): USA/OSPHL10236/2025



Target: 5350 samples       Number of changes: 142                                                   
BC: XEC.30 + XEC.2         BC BR: 13-14                    BC BR coord: 6183 - 6184          
Direction L1: <<           Initial region span: 1-13,16-142 Gap history (edge excluded): 13-16
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 7.84e-15 Rec. model vs L2: 1.65e-24                                               
Flags: Model_2BP_Bad_L1_opp

XEC.30 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.30	135	13	18.227570	NaN	NaN	NaN	*	*	*
XEC.33	169	13	17.353324	17.353324	-0.706648	4.168620e-01	*	*
XEC.35.1	28	13	16.529119	16.529119	0.941762	1.826835e-01	*	*
KP.3.1.1	12013	13	14.058814	14.058814	5.882372	1.545226e-02	*	*
JN.1.2	650	13	12.025764	12.025764	9.948472	2.019309e-03	*	*
XEC.27	25	14	11.845144	4.995777	24.008446	1.786951e-06		*
MC.1	932	13	9.774387	9.774387	14.451227	2.128336e-04	*	*
KP.2.2	1334	13	9.740843	9.740843	14.518314	2.055133e-04	*	*
NV.1	13	4	9.635840	-20.581855	75.163711	1.396469e-17
KP.3.3	1715	13	9.558425	9.558425	14.883150	1.716591e-04	*	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	16	254.645226	NaN	NaN	NaN	*	*	*
XEC.8	592	6	247.877542	227.570350	-181.140699	8.459926e-04	*
XEC.31	66	16	246.188008	226.188008	-178.376017	2.128336e-04	*	*
XEC.9	305	16	245.757797	219.674982	-165.349964	3.152184e-07		*
XEC.28	39	16	245.722025	225.722025	-177.444049	1.330215e-04	*	*
XEC.29	135	16	245.681045	217.117967	-160.235935	2.449002e-08		*
XEC.14	193	6	245.674335	225.329662	-176.659324	9.006310e-05	*
XEC.19	59	16	245.468024	225.468024	-176.936048	1.035972e-04	*	*
XEC.17	13	6	244.461986	224.101646	-174.203293	2.632478e-05	*
XEC.2.3	28	16	243.530331	215.172045	-156.344090	3.484295e-09		*

Target sequence

, 241_C|T, 344_C|T, 670_T|G, 897_C|A, 1281_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6334_T|C, 7385_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26078_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G,
26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28511_C|T, 28639_C|A, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C

 Case 72 (XEC): USA/PA-CDC-LC1136045/2025



Target: 5350 samples      Number of changes: 143                                                   
BC: XEC.29 + XEC.39       BC BR: 11-12                    BC BR coord: 4330 - 4331          
Direction L1: <<          Initial region span: 1-11,18-143 Gap history (edge excluded): 11-18
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 6.54e-01                                                            
Rec. model vs L1: 2.29e-15 Rec. model vs L2: 3.66e-07                                               
Flags: Model_1BP_Best

XEC.29 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.29	135	11	24.521489	NaN	NaN	NaN	*	*	*
XEC.9	305	11	22.952481	22.952481	-21.904962	2.080452e-01	*	*
XEC.5	126	13	15.744161	11.405366	1.189268	2.014781e-06
KP.3.1.1	12013	13	15.671634	12.108195	-0.216389	4.077608e-06
XEC.30	135	13	15.617739	11.347936	1.304127	1.906960e-06
MC.24	831	11	15.235110	15.235110	-6.470219	9.280593e-05	*	*
XEC.8	592	13	14.832127	11.347409	1.305181	1.897449e-06
KP.3.1	1957	11	13.501014	13.501014	-3.002028	1.637098e-05	*	*
KP.2.15	253	13	12.593569	7.569547	8.860906	4.352197e-08
XEC.11	16	13	12.300046	5.897558	12.204885	8.192883e-09

|||||

XEC.39 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.39	155	18	258.151444	NaN	NaN	NaN	*	*	*
KP.3.3	1715	18	256.051133	227.003390	-170.006780	5.181010e+00	*	*
XEC.31	66	18	255.067225	222.279959	-160.559919	4.595926e-02	*	*
XEC.2.1	265	18	254.687825	214.074118	-144.148235	1.255992e-05	*	*
XEC.29	135	18	254.626899	207.842734	-131.685468	2.473615e-08		*
XEC.9	305	18	254.498261	215.628180	-147.256359	5.947229e-05	*	*
XEC.28	39	18	254.424695	214.662889	-145.325779	2.265794e-05	*	*
XEC.19	59	18	254.173774	214.598744	-145.197488	2.123202e-05	*	*
XEC.14	193	18	254.136049	221.348784	-158.697567	1.813340e-02	*	*
XEC.2	921	18	254.112980	226.521723	-169.043447	3.189933e+00	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2462_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5869_C|T, 6183_A|G, 6402_C|T, 6693_A|G, 7842_A|G, 8140_C|T, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10870_G|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29461_T|C, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/CA-LACPHL-AY11147/2025



Target: 5350 samples      Number of changes: 145                                                   
BC: XEC.33 + XEC.2        BC BR: 14-15                    BC BR coord: 7842 - 7843          
Direction L1: <<          Initial region span: 1-14,16-145 Gap history (edge excluded): 14-16
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 9.90e-01                                                            
Rec. model vs L1: 5.46e-32 Rec. model vs L2: 3.98e-24                                               
Flags: Model_1BP_Best

XEC.33 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.33	169	14	17.783166	NaN	NaN	NaN	*	*	*
XEC.4	192	14	17.681102	17.681102	-3.362204	9.003245e-01	*	*
XEC.16	23	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.4.3	10	12	15.079158	-7.384864	46.769728	1.171677e-11
XEC.32	42	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.17	13	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.22	23	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.18.3	13	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.24	11	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.25	13	12	15.079158	8.682101	14.635797	1.111089e-04	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	16	271.351893	NaN	NaN	NaN	*	*	*
XEC.14	193	28	245.024085	230.424664	-184.849328	3.710592e-14
XEC.29	135	16	242.299684	232.299684	-188.599368	2.419610e-13		*
XEC.25	13	28	237.617708	216.556357	-157.112714	3.513813e-20
XEC.30	135	28	234.867262	220.260406	-164.520813	1.428367e-18
XEC.2.1	265	28	229.985151	205.687253	-135.374506	6.683403e-25
XEC.5	126	28	227.124600	212.525180	-149.050360	6.245568e-22
XEC.18	165	28	226.505286	211.905866	-147.811731	3.359768e-22
XEC.9	305	24	225.734380	215.706172	-155.412344	1.501856e-20
XEC.39	155	5	223.777073	209.859526	-143.719052	4.346875e-23

Target sequence

 Case 72 (XEC): USA/PA-CDC-LC1136147/2025



Target: 5350 samples      Number of changes: 143                                                   
BC: JN.1 + XEC.2          BC BR: 23-24                    BC BR coord: 11047 - 11048        
Direction L1: <<          Initial region span: 1-23,25-143 Gap history (edge excluded): 23-25
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 8.38e-04                                                            
Rec. model vs L1: 5.50e-37 Rec. model vs L2: 2.27e-15                                               
Flags: Model_1BP_Best

JN.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1	17255	23	38.964896	NaN	NaN	NaN	*	*	*
JN.1.20	66	21	37.160733	30.749040	-7.498080	2.705645e-04	*
JN.1.7.5	427	23	35.922361	35.922361	-17.844722	4.759631e-02	*	*
JN.1.13.1	751	21	34.713774	28.302081	-2.604161	2.334798e-05	*
LF.4	38	23	33.218853	33.218853	-12.437707	3.198735e-03	*	*
JN.1.4	8971	23	32.984622	32.984622	-11.969244	2.528826e-03	*	*
KP.1.1	593	21	32.870851	26.459158	1.081684	3.708066e-06
LB.1.3.1	292	23	32.739976	32.739976	-11.479952	1.979324e-03	*	*
JN.1.4.6	167	21	31.945957	25.534263	2.931473	1.470365e-06
XDY.3	16	13	27.833353	7.413717	39.172567	1.986137e-14

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	25	248.985986	NaN	NaN	NaN	*	*	*
XEC.9	305	4	239.296957	218.982638	-189.965275	2.061154e-09
XEC.8	592	4	239.081990	226.050856	-204.101712	2.412131e-06
XEC.29	135	25	234.694456	224.694456	-201.388913	6.222026e-07		*
XEC.18	165	40	233.975527	206.282372	-164.564745	6.257473e-15
XEC.4	192	40	233.775322	206.076946	-164.153891	5.097633e-15
XEK.5	28	25	232.964077	222.964077	-197.928154	1.103068e-07		*
XEC.2.2	273	25	232.209266	222.209266	-196.418532	5.184538e-08		*
XEC.39	155	4	227.394284	214.362558	-180.725116	2.030813e-11
XEC.31	66	40	227.359801	209.973397	-171.946794	2.518356e-13

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9120_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T,
10447_G|A, 10449_C|A, 11005_C|T, 11042_G|T, 11243_G|A, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 15951_C|T, 16887_C|T, 17410_C|T,
18109_C|T, 18163_A|G, 18395_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26029_C|A, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/SC-CDC-2-8448555/2025



Target: 5350 samples       Number of changes: 144                                                 
BC: KS.1.1.1 + XEC.13      BC BR: 4-5                     BC BR coord: 896 - 897           
Direction L1: <<           Initial region span: 1-4,10-144 Gap history (edge excluded): 4-10
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  -                                                                             
Rec. model vs L1: 5.21e-147 Rec. model vs L2: 5.92e-09                                             
Flags: Model_2BP_Bad_L1_opp

KS.1.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KS.1.1.1	20	4	13.218879	NaN	NaN	NaN	*	*	*
JN.1.53	62	4	11.072687	11.072687	-14.145374	0.117068	*	*
KP.3.1.3	46	4	10.134678	10.134678	-12.269355	0.045730	*	*
JN.1.21	60	4	9.852167	9.852167	-11.704335	0.034390	*	*
KR.1	62	4	9.026165	9.026165	-10.052329	0.015071	*	*
KP.2.3.3	149	4	8.155586	8.155586	-8.311173	0.006314	*	*
NY.15	216	4	7.866899	7.866899	-7.733798	0.004724	*	*
KP.3.2.3	759	4	7.676542	7.676542	-7.353083	0.003907	*	*
JN.1.16.1	466	4	7.084762	7.084762	-6.169525	0.002166	*	*
NY.13	463	4	7.071031	7.071031	-6.142063	0.002133	*	*

|||||

XEC.13 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.13	30	10	260.771155	NaN	NaN	NaN	*	*	*
XEC.2	921	10	254.284706	225.364714	-146.729428	1.285118e-10		*
XEC.14	193	10	251.084775	238.452271	-172.904541	6.189940e-05	*	*
XEC.8	592	10	250.518260	237.873860	-171.747721	3.483110e-05	*	*
KP.3.3	1715	10	245.519445	228.327809	-152.655618	2.492449e-09		*
XEC.40	52	10	235.248580	214.979366	-125.958732	3.970041e-15		*
XEC.25	13	10	233.442831	220.810326	-137.620652	1.351238e-12		*
XEC.4	192	10	232.866614	220.234109	-136.468218	7.603481e-13		*
XEC.36	30	10	232.239472	219.606968	-135.213935	4.049552e-13		*
XEC.28	39	10	231.672960	219.014479	-134.028958	2.244777e-13		*

Target sequence

, 241_C|T, 599_G|A, 670_T|G, 897_C|A, 1567_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3354_G|A, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G,
18449_G|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20811_T|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25571_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26625_C|T, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29296_C|T, 29510_A|C, 29700_A|G

 Case 72 (XEC): USA/SC-CDC-LC1134656/2025



Target: 5350 samples       Number of changes: 141                                                       
BC: XEC.18 + XEC.27        BC BR: 131-132                    BC BR coord: 28311 - 28312          
Direction L1: >>           Initial region span: 1-131,133-141 Gap history (edge excluded): 131-133
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 9.62e-17 Rec. model vs L2: 2.87e-44                                                   
Flags: Model_2BP_Bad_L1_opp

XEC.18 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.18	165	131	271.688833	NaN	NaN	NaN	*	*	*
XEC.8	592	141	268.317616	265.146982	-256.293964	1.437284e-03	*
XEC.30	135	138	263.288840	262.725065	-251.450130	1.278056e-04	*
XEC.24	11	131	260.788452	260.788452	-247.576903	1.845823e-05	*	*
XEC.36	30	138	260.613602	260.004365	-246.008729	8.419164e-06
XEC.2	921	141	260.553750	257.833657	-241.667314	9.612801e-07
XEC.17	13	138	259.424370	258.815133	-243.630265	2.561289e-06
XEC.32	42	138	256.181274	255.572037	-237.144074	9.980975e-08
MC.24.1	25	131	256.095961	256.095961	-238.191921	1.687243e-07		*
XEC.4	192	138	255.591885	255.008924	-236.017848	5.701223e-08

|||||

XEC.27 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.27	25	133	17.509500	NaN	NaN	NaN	*	*	*
XEC.40	52	133	17.289559	7.289559	5.420882	0.802519	*	*
PG.4	14	133	16.831188	6.831188	6.337624	0.506617	*	*
XEC.15	127	133	15.487799	5.487799	9.024402	0.132655	*	*
KP.3.3	1715	133	14.754545	4.754545	10.490911	0.063609	*	*
XEC.2.1	265	133	14.696635	4.696635	10.606729	0.059905	*	*
KP.3.3.3	288	133	14.512208	4.512208	10.975585	0.049787	*	*
KP.3.3.4	292	133	13.929129	3.929129	12.141742	0.027876	*	*
XEC.8	592	133	13.170634	3.170634	13.658732	0.013037	*	*
XEC.2	921	133	12.720093	2.720093	14.559813	0.008312	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10078_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17339_C|T, 17410_C|T, 18163_A|G, 18492_A|G,
18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T,
26846_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28329_G|A, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28958_C|A, 29421_C|T, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/SD-CDC-2-8398256/2025



Target: 5350 samples       Number of changes: 145                                               
BC: JN.1.59 + XEC.14       BC BR: 4-5                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-4,6-145 Gap history (edge excluded): 4-6
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 1.22e-105 Rec. model vs L2: 9.13e-16                                           
Flags: Model_2BP_Bad_L1_opp

JN.1.59 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.59	77	4	6.038966	NaN	NaN	NaN	*	*	*
JN.1.7	1974	4	4.716446	4.716446	-1.432892	2.658030e-01	*	*
KP.2	1589	4	3.002048	3.002048	1.995904	4.783489e-02	*	*
LB.1.7	1971	4	2.791065	2.791065	2.417870	3.877421e-02	*	*
BF.7.24	444	3	2.063169	-7.936831	23.873662	8.525790e-07		*
BQ.1.1.7	1146	3	1.807521	-8.192479	24.384959	6.606775e-07		*
JN.1	17255	4	1.715084	1.715084	4.569833	1.323355e-02	*	*
BA.2.3.2	372	3	1.534247	-8.465753	24.931506	5.018322e-07		*

|||||

XEC.14 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.14	193	6	240.295382	NaN	NaN	NaN	*	*	*
XEC.4	192	6	239.727092	229.727092	-153.454184	5.655254e-01	*	*
XEC.9	305	6	234.491446	224.491446	-142.982892	3.012455e-03	*	*
XEC.33	169	6	232.632946	222.632946	-139.265893	4.713074e-04	*	*
XEC.2	921	15	230.378687	206.576245	-107.152490	4.994993e-11
XEC.17	13	6	227.101708	217.101708	-128.203415	1.859877e-06		*
XEC.2.2	273	15	226.754570	194.754347	-83.508695	3.674296e-16
XEC.15	127	6	226.032571	216.032571	-126.065142	6.411515e-07		*
XEC.2.1	265	36	225.453383	196.765848	-87.531697	2.742244e-15
KP.3.3	1715	4	224.481700	220.880935	-135.761870	8.149246e-05	*

Target sequence

, 241_C|T, 670_T|G, 733_T|C, 897_C|A, 1348_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7644_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11124_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 14646_T|G, 14868_T|C, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19324_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20436_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25655_T|C,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/TN-CDC-LC1135518/2025



Target: 5350 samples      Number of changes: 145                                                 
BC: XEC.4.3 + XEC.2       BC BR: 11-12                   BC BR coord: 4387 - 4388         
Direction L1: <<          Initial region span: 1-8,13-145 Gap history (edge excluded): 8-13
Alt. candidates: [], []                                                                                 
Model 1BP/2BP comparison: 1BP vs 2BP: 1.76e-02                                                          
Rec. model vs L1: 4.38e-36 Rec. model vs L2: 1.07e-17                                             
Flags: Model_1BP_Best

XEC.4.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4.3	10	8	19.322509	NaN	NaN	NaN	*	*	*
XEC.17	13	8	19.322509	11.469367	-0.938735	1.0	*	*
XEC.18.3	13	8	19.322509	11.469367	-0.938735	1.0	*	*
XEC.4.1.4	23	8	19.322509	11.469367	-0.938735	1.0	*	*
XEC.16	23	8	19.322509	11.469367	-0.938735	1.0	*	*
XEC.22	23	8	19.322509	11.469367	-0.938735	1.0	*	*
XEC.24	11	8	19.322509	11.469367	-0.938735	1.0	*	*
XEC.25	13	8	19.322509	11.469367	-0.938735	1.0	*	*
XEC.8.1	12	8	19.322509	11.469367	-0.938735	1.0	*	*
XEC.32	42	8	19.322509	11.469367	-0.938735	1.0	*	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	13	242.091895	NaN	NaN	NaN	*	*	*
XEC.14	193	3	231.964442	221.623149	-155.246297	2.851729e-05	*
XEC.13	30	1	231.121914	219.686448	-151.372897	4.098047e-06
XEC.15	127	1	230.572144	219.200663	-150.401327	2.523156e-06
XEC.29	135	14	228.813573	208.426465	-128.852930	5.277413e-11		*
XEC.4	192	1	227.715782	216.304723	-144.609446	1.395281e-07
XEC.30	135	1	224.844883	213.496946	-138.993893	8.400287e-09
XEC.2.1	265	13	221.487393	211.487393	-134.974787	1.125543e-09		*
XEC.32	42	1	220.173020	208.703653	-129.407306	6.982703e-11
XEC.33	169	28	218.514240	204.157655	-120.315309	7.415751e-13

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3871_G|C, 4184_G|A, 4321_C|T, 5720_G|A, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10323_A|G, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11530_C|T, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15735_T|C, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19493_G|A, 19716_C|T, 19955_C|T, 20055_A|G, 20555_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29095_C|T, 29409_C|T, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/TN-SPHL-1120/2025



Target: 5350 samples       Number of changes: 146                                                       
BC: KP.3.3 + KP.2.2        BC BR: 142-143                    BC BR coord: 28883 - 28884          
Direction L1: >>           Initial region span: 1-137,143-146 Gap history (edge excluded): 137-143
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 7.77e-06 Rec. model vs L2: 1.25e-91                                                   
Flags: Model_2BP_Bad_L1_opp

KP.3.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.3	1715	137	230.577621	NaN	NaN	NaN	*	*	*
XEC.8	592	143	224.941378	221.333078	-138.666156	4.274877e-03	*
XEC.32	42	143	219.836446	216.228146	-128.456292	2.593285e-05	*
XEC.33	169	137	218.993436	215.209734	-126.419468	9.351255e-06		*
XEC.4	192	137	218.547775	214.743732	-125.487465	5.873852e-06		*
XEC.31	66	137	218.028254	214.235219	-124.470439	3.527222e-06		*
XEC.14	193	143	214.782719	211.174419	-118.348837	1.653833e-07
XEC.24	11	137	211.567155	201.586271	-99.172541	1.131378e-11		*
XEC.18	165	137	211.024563	201.565082	-99.130165	1.108975e-11		*
XEC.36	30	137	210.783068	207.005301	-110.010603	2.555546e-09		*

|||||

KP.2.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.2	1334	143	9.703448	NaN	NaN	NaN	*	*	*
BE.5	231	144	7.942662	-2.057338	12.114676	7.810825e-06		*
XEC.32	42	138	5.881863	-3.995542	15.991085	1.122446e-06
BQ.1.10	2048	144	5.637057	-4.362943	16.725885	7.753122e-07		*
BQ.1.1	36940	144	5.577032	-0.638570	9.277141	3.215315e-05	*	*
CH.1.1	4056	144	5.057243	-4.942757	17.885514	4.340961e-07		*
XEC.14	193	138	4.241647	-4.110738	16.221476	1.000511e-06
BA.4.1	18821	144	4.219795	-2.014633	12.029266	8.129591e-06		*
XEC.2	921	138	3.357854	-4.122734	16.245469	9.856150e-07
BA.2.12.1	107150	144	3.258876	-6.741124	21.482248	7.211527e-08		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6283_T|C, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11109_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13931_A|G, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G,
18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21697_C|T, 21711_C|T, 21718_G|A, 21738_T|C,
21765_21770, 21777_G|A, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23285_G|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23905_T|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28419_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29320_A|G, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/TX-USAFSAM-S23573/2025



Target: 5350 samples       Number of changes: 144                                               
BC: XEC.39 + MC.28.1.1     BC BR: 140-141                    BC BR coord: 28958 - 28959  
Direction L1: >>           Initial region span: 1-140,141-144 Gap history (edge excluded):
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 9.45e-16 Rec. model vs L2: 2.01e-177                                          
Flags: Model_2BP_Bad_L1_opp

XEC.39 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.39	155	140	243.880226	NaN	NaN	NaN	*	*	*
KP.3.3	1715	144	242.728929	239.080917	-172.161835	8.229747e-03	*
XEC.18	165	140	230.499372	230.499372	-154.998744	1.545752e-06		*
XEC.19	59	140	229.962991	229.962991	-153.925982	9.052995e-07		*
XEC.29	135	140	226.268740	226.268740	-146.537480	2.249439e-08		*
XEC.15	127	140	225.086160	225.086160	-144.172320	6.877573e-09		*
XEC.36	30	140	223.100395	223.100395	-140.200790	9.448452e-10		*
XEC.8	592	143	222.587547	218.677428	-131.354857	1.131378e-11
XEC.4	192	140	222.050643	222.050643	-138.101287	3.306370e-10		*
XEC.38	34	140	222.033037	222.033037	-138.066074	3.257145e-10		*

|||||

MC.28.1.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.28.1.1	129	141	9.672369	NaN	NaN	NaN	*	*	*
BF.30	60	142	8.072392	-1.927608	13.855216	9.166088e-06		*
BQ.2	47	142	7.991120	-2.008880	14.017760	8.461365e-06		*
BA.2.10.2	48	141	7.665913	7.665913	-5.331826	1.346603e-01	*	*
JC.5	136	142	7.493066	-8.808982	27.617964	9.424059e-09		*
XBB.1.5.75	85	141	7.399568	7.399568	-4.799137	1.033122e-01	*	*
JC.5.1	53	142	7.314594	-8.932458	27.864915	8.358390e-09		*
LB.1.4	235	141	7.006154	7.006154	-4.012308	6.959935e-02	*	*
JN.1.32.1	55	142	6.823753	-3.176247	16.352494	2.639292e-06		*
JN.1.18.2	51	141	6.690809	6.690809	-3.381617	5.079283e-02	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6040_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 15921_G|T, 16332_C|T, 17410_C|T, 18163_A|G,
18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20946_C|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23383_G|A, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26176_C|T, 26270_C|T, 26289_T|C, 26529_G|C, 26577_C|G, 26610_A|G,
26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C,
28884_G|C, 28958_C|A, 29272_C|T, 29510_A|C, 29734_29759, 29769_C|T

 Case 72 (XEC): USA/VA-CAV_VAS3N_00022765_01/2025



Target: 5350 samples      Number of changes: 140                                               
BC: LE.1 + XEC.18         BC BR: 5-6                    BC BR coord: 672 - 673          
Direction L1: <<          Initial region span: 1-5,8-140 Gap history (edge excluded): 5-8
Alt. candidates: [], []                                                                               
Model 1BP/2BP comparison: 1BP vs 2BP: 3.87e-01                                                        
Rec. model vs L1: 4.15e-98 Rec. model vs L2: 5.48e-08                                           
Flags: Model_1BP_Best

LE.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LE.1	27	5	14.065224	NaN	NaN	NaN	*	*	*
LF.7.9.3	20	3	7.111420	-1.801681	15.603363	1.288006e-07
XFB.3	56	3	6.955858	-1.957243	15.914486	1.103068e-07
NY.12.1	17	3	6.912387	-2.000714	16.001429	1.054531e-07
XEL.5	19	3	6.879637	-2.033464	16.066928	1.018260e-07
MC.13.2.4	37	3	6.742160	-10.006521	32.013041	3.519912e-11
LC.1	10	3	6.582895	-2.330207	16.660413	7.581270e-08
XEC.35.1	28	3	6.538559	-2.374542	16.749085	7.247675e-08
LF.6	27	3	6.511211	-2.401891	16.803781	7.068729e-08
LF.7.1.11	20	3	6.449363	-2.463738	16.927476	6.623876e-08

|||||

XEC.18 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.18	165	8	291.947526	NaN	NaN	NaN	*	*	*
XEC.9	305	8	291.564307	285.175132	-280.350264	6.736800e-01	*	*
XEC.31	66	8	291.162153	284.774240	-279.548480	4.515812e-01	*	*
XEC.39	155	8	291.108436	284.729319	-279.458637	4.317105e-01	*	*
XEC.14	193	8	285.929177	271.692770	-253.385541	9.422455e-07		*
XEC.17	13	8	284.947219	278.574574	-267.149148	9.164528e-04	*	*
XEC.32	42	8	281.704123	275.331478	-260.662956	3.571285e-05	*	*
MC.24.1	25	8	281.340506	274.967861	-259.935721	2.491601e-05	*	*
XEC.4	192	8	280.978934	274.590540	-259.181080	1.703910e-05	*	*
XEC.38	34	8	280.882119	274.509473	-259.018946	1.572907e-05	*	*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 515_G|T, 670_T|G, 897_C|A, 1250_A|G, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 17502_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T,
26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/VA-USAFSAM-S23569/2025



Target: 5350 samples       Number of changes: 143                                             
BC: KP.3.1.1 + XEC.2       BC BR: 16-17                    BC BR coord: 6806 - 6807    
Direction L1: <<           Initial region span: 1-16,17-143 Gap history (edge excluded):
Alt. candidates: [], []                                                                              
Model 1BP/2BP comparison:  -                                                                         
Rec. model vs L1: 4.77e-63 Rec. model vs L2: 6.45e-25                                         
Flags: Model_2BP_Bad_L1_opp

KP.3.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.1	12013	16	15.169287	NaN	NaN	NaN	*	*	*
XEC.39	155	13	13.642950	-2.753732	41.507464	1.641615e-08
XEC.9	305	13	13.335366	-3.054843	42.109685	1.216139e-08
LB.1.3.1	292	5	6.340081	-19.620476	75.240952	7.778484e-16
BW.1.1.2	55	4	6.082585	-83.370911	202.741822	1.601850e-43
B.1.110.3	764	3	5.658809	-99.490300	234.980600	1.598802e-50
XEC.38	34	13	5.581698	-10.808511	57.617021	5.212299e-12
XEC.8.1	12	13	5.338246	-11.138974	58.277949	3.747246e-12
XEC.18.3	13	13	5.258203	-11.132006	58.264011	3.784906e-12
KP.2.2	1334	5	4.776716	-21.178024	78.356048	1.634540e-16

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	17	263.750030	NaN	NaN	NaN	*	*	*
XEC.14	193	17	256.339898	256.339898	-240.679797	6.051707e-04	*	*
XEC.9	305	2	255.763346	248.818189	-225.636378	3.280827e-07
XEC.18	165	4	255.329855	247.205583	-222.411165	6.525260e-08
XEC.31	66	17	254.103847	254.103847	-236.207693	6.474850e-05	*	*
XEC.8	592	17	247.985337	247.985337	-223.970674	1.423467e-07		*
KP.3.3	1715	8	247.348464	241.874679	-211.749358	3.160881e-10
XEC.40	52	17	246.856476	246.856476	-221.712952	4.598273e-08		*
XEC.2.1	265	17	246.672384	246.672384	-221.344769	3.821644e-08		*
XEK.1.2	33	17	245.799046	241.412235	-210.824471	1.985461e-10		*

Target sequence

, 106_C|T, 241_C|T, 601_C|T, 670_T|G, 897_C|A, 2060_G|A, 2062_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5477_C|T, 6183_A|G, 6794_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T,
22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A,
23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23191_C|T, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26155_26157, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G,
26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28085_G|T, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/VT-25-003495-WGS-01/2025



Target: 5350 samples      Number of changes: 144                                                   
BC: XEC.33 + XEC.2        BC BR: 14-15                    BC BR coord: 7842 - 7843          
Direction L1: <<          Initial region span: 1-14,16-144 Gap history (edge excluded): 14-16
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 9.90e-01                                                            
Rec. model vs L1: 4.89e-32 Rec. model vs L2: 3.98e-24                                               
Flags: Model_1BP_Best

XEC.33 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.33	169	14	17.783166	NaN	NaN	NaN	*	*	*
XEC.4	192	14	17.681102	17.681102	-3.362204	9.003245e-01	*	*
XEC.16	23	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.4.3	10	12	15.079158	-7.384864	46.769728	1.171677e-11
XEC.32	42	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.17	13	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.22	23	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.18.3	13	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.24	11	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.25	13	12	15.079158	8.682101	14.635797	1.111089e-04	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	16	267.720756	NaN	NaN	NaN	*	*	*
XEC.14	193	28	241.392023	226.792602	-177.585205	3.710592e-14
XEC.29	135	16	238.681067	228.681067	-181.362133	2.443927e-13		*
XEC.30	135	28	231.322752	216.715897	-157.431793	1.555087e-18
XEC.25	13	28	229.899943	208.838593	-141.677185	5.911337e-22
XEC.2.1	265	28	226.378931	202.081034	-128.162068	6.852594e-25
XEC.5	126	28	223.567610	208.968190	-141.936379	6.731998e-22
XEC.9	305	24	222.145129	212.116921	-148.233841	1.563148e-20
XEC.8	592	28	219.655610	205.052805	-134.105610	1.342397e-23
XEC.18	165	28	219.150953	204.551533	-133.103065	8.101443e-24

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 915_A|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6638_C|T, 7842_A|G, 7852_T|C, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10273_T|C, 10447_G|A, 10449_C|A, 11042_G|T, 11200_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16308_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22594_C|T, 22629_A|C, 22674_C|T,
22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A,
22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25613_C|T, 26060_C|T, 26093_A|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/VT-25-003503-WGS-01/2025



Target: 5350 samples      Number of changes: 143                                                   
BC: XEC.33 + XEC.2        BC BR: 14-15                    BC BR coord: 7842 - 7843          
Direction L1: <<          Initial region span: 1-14,16-143 Gap history (edge excluded): 14-16
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 9.90e-01                                                            
Rec. model vs L1: 4.89e-32 Rec. model vs L2: 3.98e-24                                               
Flags: Model_1BP_Best

XEC.33 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.33	169	14	17.783166	NaN	NaN	NaN	*	*	*
XEC.4	192	14	17.681102	17.681102	-3.362204	9.003245e-01	*	*
XEC.16	23	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.4.3	10	12	15.079158	-7.384864	46.769728	1.171677e-11
XEC.32	42	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.17	13	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.22	23	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.18.3	13	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.24	11	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.25	13	12	15.079158	8.682101	14.635797	1.111089e-04	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	16	267.271358	NaN	NaN	NaN	*	*	*
XEC.14	193	27	241.392023	226.343204	-176.686408	3.710592e-14
XEC.29	135	16	238.231668	228.231668	-180.463337	2.443927e-13		*
XEC.30	135	27	231.322752	216.266498	-156.532997	1.555087e-18
XEC.25	13	27	229.899943	208.389194	-140.778389	5.911337e-22
XEC.2.1	265	27	226.378931	201.639197	-127.278394	6.921464e-25
XEC.5	126	27	223.567610	208.518791	-141.037583	6.731998e-22
XEC.9	305	23	222.145129	211.667522	-147.335045	1.570984e-20
XEC.8	592	27	219.655610	204.603407	-133.206814	1.342397e-23
XEC.18	165	27	219.150953	204.102134	-132.204269	8.101443e-24

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 915_A|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6638_C|T, 7842_A|G, 7852_T|C, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10198_C|T, 10273_T|C, 10447_G|A, 10449_C|A, 11042_G|T, 11200_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16308_C|T,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22594_C|T, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25613_C|T, 26060_C|T, 26093_A|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/VT-25-003998-WGS-01/2025



Target: 5350 samples      Number of changes: 143                                                   
BC: XEC.22 + XEC.2        BC BR: 12-13                    BC BR coord: 6183 - 6184          
Direction L1: <<          Initial region span: 1-12,15-143 Gap history (edge excluded): 12-15
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 1.30e-01                                                            
Rec. model vs L1: 2.60e-51 Rec. model vs L2: 1.05e-17                                               
Flags: Model_1BP_Best

XEC.22 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.22	23	12	15.079158	NaN	NaN	NaN	*	*	*
XEC.16	23	12	15.079158	15.079158	-6.158317	1.000000	*	*
XEC.4.3	10	12	15.079158	15.079158	-6.158317	1.000000	*	*
XEC.32	42	12	15.079158	15.079158	-6.158317	1.000000	*	*
XEC.17	13	12	15.079158	15.079158	-6.158317	1.000000	*	*
XEC.18.3	13	12	15.079158	15.079158	-6.158317	1.000000	*	*
XEC.25	13	12	15.079158	15.079158	-6.158317	1.000000	*	*
XEC.24	11	12	15.079158	15.079158	-6.158317	1.000000	*	*
XEC.4.1	68	12	15.049528	15.049528	-6.099057	0.970446	*	*
XEC.13	30	12	15.045257	15.045257	-6.090514	0.965605	*	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	15	267.720756	NaN	NaN	NaN	*	*	*
XEC.14	193	27	241.392023	213.189659	-142.379318	3.692085e-14
XEC.29	135	15	238.681067	206.515046	-129.030091	4.659679e-17		*
XEC.30	135	27	231.322752	203.112954	-122.225907	1.555087e-18
XEC.25	13	27	229.899943	195.235649	-106.471299	5.881854e-22
XEC.2.1	265	27	226.378931	188.478091	-92.956182	6.852594e-25
XEC.5	126	27	223.567610	195.365246	-106.730493	6.698422e-22
XEC.9	305	23	222.145129	192.431162	-100.862325	3.558920e-23
XEC.8	592	27	219.655610	191.451553	-98.903105	1.335702e-23
XEC.18	165	27	219.150953	190.954669	-97.909337	8.142052e-24

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 915_A|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6638_C|T, 7852_T|C, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10273_T|C, 10447_G|A, 10449_C|A, 11042_G|T, 11200_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16308_C|T,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22594_C|T, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25613_C|T, 26060_C|T, 26093_A|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): USA/CA-LACPHL-AY11147/2025



Target: 5350 samples      Number of changes: 145                                                   
BC: XEC.33 + XEC.2        BC BR: 14-15                    BC BR coord: 7842 - 7843          
Direction L1: <<          Initial region span: 1-14,16-145 Gap history (edge excluded): 14-16
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 9.90e-01                                                            
Rec. model vs L1: 5.46e-32 Rec. model vs L2: 3.98e-24                                               
Flags: Model_1BP_Best

XEC.33 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.33	169	14	17.783166	NaN	NaN	NaN	*	*	*
XEC.4	192	14	17.681102	17.681102	-3.362204	9.003245e-01	*	*
XEC.16	23	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.4.3	10	12	15.079158	-7.384864	46.769728	1.171677e-11
XEC.32	42	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.17	13	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.22	23	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.18.3	13	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.24	11	12	15.079158	8.682101	14.635797	1.111089e-04	*
XEC.25	13	12	15.079158	8.682101	14.635797	1.111089e-04	*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	16	271.351893	NaN	NaN	NaN	*	*	*
XEC.14	193	28	245.024085	230.424664	-184.849328	3.710592e-14
XEC.29	135	16	242.299684	232.299684	-188.599368	2.419610e-13		*
XEC.25	13	28	237.617708	216.556357	-157.112714	3.513813e-20
XEC.30	135	28	234.867262	220.260406	-164.520813	1.428367e-18
XEC.2.1	265	28	229.985151	205.687253	-135.374506	6.683403e-25
XEC.5	126	28	227.124600	212.525180	-149.050360	6.245568e-22
XEC.18	165	28	226.505286	211.905866	-147.811731	3.359768e-22
XEC.9	305	24	225.734380	215.706172	-155.412344	1.501856e-20
XEC.39	155	5	223.777073	209.859526	-143.719052	4.346875e-23

Target sequence

 Case 72 (XEC): IGS-10285-CVDP-0398E8C9-B516-48A2-86FD-3E54BF5C21F7



Target: 5350 samples       Number of changes: 144                                             
BC: KP.3.1.1 + XEC.9       BC BR: 17-18                    BC BR coord: 7090 - 7091    
Direction L1: <<           Initial region span: 1-17,18-144 Gap history (edge excluded):
Alt. candidates: [], []                                                                              
Model 1BP/2BP comparison:  -                                                                         
Rec. model vs L1: 4.62e-76 Rec. model vs L2: 3.24e-24                                         
Flags: Model_2BP_Bad_L1_opp

KP.3.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.1	12013	17	4.454387	NaN	NaN	NaN	*	*	*
BA.5.1.23	4202	4	3.636291	-62.310012	188.620023	1.010018e-29
BA.5	6418	4	3.241758	-52.349998	168.699995	2.137479e-25
BF.10	8612	4	3.031054	-75.376164	214.752327	2.139299e-35
AY.4.2.2	19573	3	3.012210	-92.753561	249.507121	6.056663e-43
BQ.1.1	36940	4	2.419308	-50.695834	165.391668	1.118560e-24
XBB.1.16.6	4784	4	2.033307	-65.997527	195.995054	2.522216e-31
BA.5.1	53705	4	1.871199	-44.187545	152.375091	7.477302e-22
BA.2	443141	4	1.075408	-39.273974	142.547949	1.019301e-19
P.1	10221	3	1.032244	-128.975452	321.950905	1.127424e-58

|||||

XEC.9 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.9	305	18	277.842271	NaN	NaN	NaN	*	*	*
XEC.13	30	14	273.572892	262.580198	-263.160397	2.358665e-07
XEC.2	921	17	269.368766	265.772089	-269.544179	5.728826e-06		*
XEC.16	23	17	266.523748	262.913957	-263.827913	3.297273e-07		*
XEC.31	66	17	262.279959	258.670168	-255.340337	4.726882e-09		*
XEC.28	39	17	261.637429	258.027638	-254.055277	2.492449e-09		*
XEC.19	59	17	261.386508	257.776717	-253.553434	1.931440e-09		*
XEC.14	193	17	261.348784	257.738993	-253.477985	1.865009e-09		*
XEC.17	13	17	260.351159	256.741368	-251.482737	6.860984e-10		*
XEC.8	592	17	260.218741	256.608950	-251.217899	6.024599e-10		*

Target sequence

, 241_C|T, 379_C|T, 509_G|A, 670_T|G, 897_C|A, 2030_G|A, 2060_G|A, 2790_C|T, 3037_C|T, 3177_C|T, 3431_G|T, 3565_T|C, 3736_C|T, 4184_G|A, 4321_C|T, 5184_C|A, 6183_A|G, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13372_C|T, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21595_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): IGS-10285-CVDP-336E7E7C-A753-4F02-8767-9C96D4FFF043



Target: 5350 samples       Number of changes: 145                                               
BC: KP.2.3.13 + XEC.14     BC BR: 5-6                    BC BR coord: 1297 - 1298        
Direction L1: <<           Initial region span: 1-5,9-145 Gap history (edge excluded): 5-9
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 9.57e-156 Rec. model vs L2: 1.49e-23                                           
Flags: Model_2BP_Bad_L1_opp

KP.2.3.13 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3.13	25	5	11.399879	NaN	NaN	NaN	*	*	*
XEC.4.3	10	4	10.581513	0.581513	8.836974	0.000020	*	*
KP.3.3.10	55	4	9.569912	-0.430088	10.860176	0.000007		*
JN.1.34	83	4	8.927300	-1.072700	12.145400	0.000004		*
KS.2	18	4	8.837955	-1.162045	12.324089	0.000004		*
MC.10	221	4	8.648716	-1.351284	12.702569	0.000003		*
JN.1.40	26	4	8.488168	-1.511832	13.023663	0.000002		*
LZ.1	28	4	8.453281	-1.546719	13.093438	0.000002		*
LF.7.1	165	5	8.288343	8.288343	-6.576686	0.044601	*	*
NY.7	36	4	8.201967	-1.798033	13.596067	0.000002		*

|||||

XEC.14 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.14	193	9	269.682855	NaN	NaN	NaN	*	*	*
XEC.2	921	8	256.626219	236.626219	-173.252439	5.135572e-14		*
XEC.2.2	273	9	249.494751	219.494751	-138.989503	1.866914e-21		*
XEC.4	192	9	248.969849	235.256251	-170.512501	1.304985e-14		*
KP.3.3	1715	9	248.613194	230.342798	-160.685596	9.620984e-17		*
XEC.28	39	9	247.386239	233.672640	-167.345279	2.687943e-15		*
XEC.8	592	9	245.830690	232.105196	-164.210393	5.592137e-16		*
XEC.29	135	9	241.851981	228.138382	-156.276764	1.060719e-17		*
XEC.17	13	9	240.815307	227.101708	-154.203415	3.749159e-18		*
MC.24.1	25	9	237.862520	223.494994	-146.989989	1.019301e-19		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1150_C|T, 1288_C|T, 1973_C|T, 2060_G|A, 2650_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10156_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11752_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13554_C|T, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20544_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23609_C|T, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): IGS-10285-CVDP-3F05C326-1A96-41EB-A33D-E8C815FBAD27



Target: 5350 samples       Number of changes: 148                                                 
BC: JN.1.7.5 + XEC.2       BC BR: 16-17                   BC BR coord: 4387 - 4388         
Direction L1: <<           Initial region span: 1-7,18-148 Gap history (edge excluded): 7-18
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  -                                                                             
Rec. model vs L1: 3.93e-121 Rec. model vs L2: 2.93e-39                                             
Flags: Model_2BP_Bad_L1_opp

JN.1.7.5 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.7.5	427	7	28.134461	NaN	NaN	NaN	*	*	*
JN.2	574	5	18.992844	-17.389622	70.779244	2.307954e-16
BA.4.1	18821	6	8.227998	-18.361891	72.723781	8.749063e-17		*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	18	237.681481	NaN	NaN	NaN	*	*	*
XEC.8	592	20	225.436821	209.046612	-130.093225	8.070907e-09
XEC.14	193	24	223.343498	205.993885	-123.987770	3.822295e-10
XEC.9	305	24	222.826061	209.459085	-130.918170	1.222235e-08
XEC.4	192	24	217.444787	209.930296	-131.860591	1.955568e-08
XEC.33	169	9	216.080219	197.721356	-107.442712	9.739515e-14
XEC.30	135	20	213.698307	197.308098	-106.616197	6.463631e-14
XEC.31	66	24	210.925853	193.576240	-99.152479	1.543074e-15
XEK.1	88	24	210.797798	185.434540	-82.869081	4.500177e-19
XEC.29	135	24	210.500397	179.153884	-70.307768	8.430635e-22

Target sequence

, 241_C|T, 670_T|G, 688_.|CAT, 689_T|A, 692_T|A, 694_T|G, 897_C|A, 958_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4276_C|T, 4321_C|T, 5512_C|T, 6183_A|G, 6543_C|T,
7842_A|G, 8293_C|T, 8393_G|A, 9298_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18891_G|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23222_G|A,
23271_C|T, 23403_A|G, 23423_23428, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
26060_C|T, 26159_26161, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27223_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
27970_C|T, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): IGS-10285-CVDP-4CC641EA-D8D1-4993-9310-51B7F11A72A7



Target: 5350 samples      Number of changes: 151                                                                
BC: XEC.14 + JG.2 + XEC.14 BC BR: 9-10, 14-15                   BC BR coord: 3566 - 3567, 5647 - 5648     
Direction L1: <<          Initial region span: 1-9,10-14,19-151 Gap history (edge excluded): 9-19 -> 14-19
Alt. candidates: [], []                                                                                                
Model 1BP/2BP comparison: 2BP vs 1BP: 3.91e-11                                                                         
Rec. model vs L1: 4.50e-21 Rec. model vs L2: 0.00e+00                                                            
Flags: Model_2BP_Best

XEC.14 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.14	193	9	1.437887	None	None	None	*	*	*

|||||

JG.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JG.2	72	14	13.822197	NaN	NaN	NaN	*	*	*
DN.1.1	313	13	7.057412	-2.942588	29.885177	5.236644e-08		*
XBB.1	3166	13	6.520895	5.880687	12.238625	3.562065e-04	*	*
PQ.14	26	10	6.443512	-25.783951	75.567901	6.306190e-18
KP.2.25.2	16	10	6.443512	-11.409630	46.819261	1.103444e-11
XBB.1.16.1	1702	13	5.865231	-4.134769	32.269538	1.593098e-08		*
HV.1	11771	13	5.520429	5.358811	13.282378	2.117721e-04	*	*
BN.2.1	21	10	5.344899	-33.085466	90.170932	4.260076e-21
XBB.1.5.68	27	10	5.344899	-12.508243	49.016485	3.673045e-12
B.1.523	109	10	5.335683	-34.834734	93.669467	7.402902e-22

|||||

XEC.14 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.14	193	19	223.817661	NaN	NaN	NaN	*	*	*
KP.3.3	1715	19	221.579348	204.827434	-95.654869	1.949856e-03	*	*
XEC.2	921	19	220.572159	197.068229	-80.136457	8.356968e-07		*
XEC.18	165	18	217.457353	210.353067	-106.706134	4.916442e-01	*	*
XEC.29	135	18	210.590163	189.510638	-65.021276	4.352938e-10		*
XEC.9	305	19	210.340949	198.161717	-82.323433	2.485591e-06		*
XEC.8	592	19	210.278391	193.090424	-72.180848	1.561553e-08		*
XEC.13	30	19	206.824660	189.723059	-65.446118	5.397041e-10		*
XEC.2.2	273	25	206.133276	166.186123	-18.372247	3.227481e-20
XEC.4	192	19	205.048200	187.922193	-61.844386	8.876755e-11		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1848_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3619_C|T, 3644_G|A, 4184_G|A, 4321_C|T, 5646_C|T, 5806_C|T, 6183_A|G, 6478_T|C, 7420_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9445_T|C, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C,
13585_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21812_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23644_C|A, 23854_C|A, 23948_G|T, 24367_A|G, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T,
25006_C|T, 25207_C|T, 25584_C|T, 25603_C|A, 25703_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26645_C|T, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): IGS-10285-CVDP-5514ABAB-1EBE-40B9-AD35-BB8653DA8DC4



Target: 5350 samples      Number of changes: 142                                                        
BC: XEC.2 + XEC.1 + XEC.2 BC BR: 4-5, 6-7                   BC BR coord: 1153 - 1154, 2060 - 2061
Direction L1: <<          Initial region span: 1-4,5-6,7-142 Gap history (edge excluded): 4-7 ->  
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison: 2BP vs 1BP: 1.76e-05                                                                 
Rec. model vs L1: 6.09e-10 Rec. model vs L2: 5.45e-37                                                    
Flags: Model_2BP_Best

XEC.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	4	4.922764	None	None	None	*	*	*

|||||

XEC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.1	99	6	8.426421	NaN	NaN	NaN	*	*	*
XEC.5	126	6	7.502265	7.502265	-5.004529	3.965314e-01	*	*
XEC.30	135	6	7.403194	7.403194	-4.806389	3.605949e-01	*	*
XEC.4	192	6	7.081051	7.081051	-4.162102	2.605397e-01	*	*
HC.1	10	5	6.052145	-3.947855	17.895709	4.222851e-06		*
HC.2	19	5	6.052145	-13.664830	37.329660	2.549382e-10		*
B.1.558	181	5	6.052145	-3.947855	17.895709	4.222851e-06		*
B.1.385	53	5	6.052145	-14.191177	38.382354	1.508101e-10		*
BF.7.5.1	141	5	6.045028	-6.944386	23.888773	2.112972e-07		*
B.1.1.251	36	5	6.023975	-3.976025	17.952051	4.118589e-06		*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	7	276.776131	NaN	NaN	NaN	*	*	*
KP.3.3	1715	8	268.793520	263.786093	-227.572186	1.658114e-08		*
XEC.39	155	8	268.305693	253.011567	-206.023135	3.468098e-13		*
XEC.28	39	8	267.386239	252.026439	-204.052877	1.295124e-13		*
XEC.33	169	8	266.989165	251.678096	-203.356193	9.172330e-14		*
XEC.8	592	8	264.881989	249.531997	-199.063994	1.068431e-14		*
XEC.14	193	8	261.797265	246.489946	-192.979892	5.110828e-16		*
XEC.17	13	8	260.815307	245.534126	-191.068251	1.966709e-16		*
MC.24.1	25	8	257.862520	242.540517	-185.081034	9.840748e-18		*
XEC.15	127	8	257.700818	242.403764	-184.807527	8.598018e-18		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1150_C|T, 1288_C|T, 2060_G|A, 2650_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10156_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20544_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28896_C|T, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): IGS-10285-CVDP-5D565D61-4013-4E04-BC27-A4C69F4AEB42



Target: 5350 samples      Number of changes: 148                                                               
BC: XEC.14 + JG.2 + XEC.14 BC BR: 8-9, 13-14                   BC BR coord: 3566 - 3567, 5647 - 5648     
Direction L1: <<          Initial region span: 1-8,9-13,17-148 Gap history (edge excluded): 8-17 -> 13-17
Alt. candidates: [], []                                                                                               
Model 1BP/2BP comparison: 2BP vs 1BP: 4.25e-14                                                                        
Rec. model vs L1: 4.50e-21 Rec. model vs L2: 0.00e+00                                                           
Flags: Model_2BP_Best

XEC.14 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.14	193	8	11.437887	None	None	None	*	*	*

|||||

JG.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JG.2	72	13	13.822197	NaN	NaN	NaN	*	*	*
DN.1.1	313	12	7.057412	-2.942588	27.885177	5.236644e-08		*
XBB.1	3166	12	6.520895	5.880687	10.238625	3.562065e-04	*	*
KP.2.25.2	16	9	6.443512	-11.409630	44.819261	1.103444e-11
PQ.14	26	9	6.443512	-25.783951	73.567901	6.306190e-18
XBB.1.16.1	1702	12	5.865231	-4.134769	30.269538	1.593098e-08		*
KP.3.1.1	12013	14	5.674926	2.067218	17.865564	7.849977e-06		*
HV.1	11771	12	5.520429	5.358811	11.282378	2.117721e-04	*	*
BN.2.1	21	9	5.344899	-33.085466	88.170932	4.260076e-21
XBB.1.5.68	27	9	5.344899	-12.508243	47.016485	3.673045e-12

|||||

XEC.14 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.14	193	17	233.817661	NaN	NaN	NaN	*	*	*
KP.3.3	1715	17	231.579348	225.503108	-143.006215	3.473526e-02	*	*
XEC.29	135	16	220.590163	219.510638	-131.021276	8.653168e-05	*	*
XEC.9	305	17	220.340949	217.110534	-126.221067	7.849977e-06		*
XEC.8	592	17	220.278391	223.090424	-138.180848	3.104198e-03	*	*
XEC.2	921	17	218.963593	205.513627	-103.027254	7.231424e-11		*
XEC.2.2	273	23	216.133276	196.186123	-84.372247	6.415881e-15
XEC.4	192	17	215.048200	217.922193	-127.844386	1.764603e-05	*	*
XEC.18	165	16	214.822419	227.718133	-147.436266	3.182239e-01	*	*
XEC.40	52	17	214.499918	217.393383	-126.786765	1.043860e-05	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3619_C|T, 3644_G|A, 4184_G|A, 4321_C|T, 5646_C|T, 6183_A|G, 6478_T|C, 7420_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9445_T|C, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21812_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23644_C|A, 23854_C|A, 23948_G|T, 24367_A|G, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
25603_C|A, 25703_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26645_C|T, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): IGS-10285-CVDP-7035C5F5-2143-4E09-9861-E8C8C4DF8C86



Target: 5350 samples       Number of changes: 146                                               
BC: KP.2.3.13 + XEC.14     BC BR: 5-6                    BC BR coord: 1297 - 1298        
Direction L1: <<           Initial region span: 1-5,9-146 Gap history (edge excluded): 5-9
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 9.57e-156 Rec. model vs L2: 1.49e-23                                           
Flags: Model_2BP_Bad_L1_opp

KP.2.3.13 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3.13	25	5	11.399879	NaN	NaN	NaN	*	*	*
XEC.4.3	10	4	10.581513	0.581513	8.836974	0.000020	*	*
KP.3.3.10	55	4	9.569912	-0.430088	10.860176	0.000007		*
JN.1.34	83	4	8.927300	-1.072700	12.145400	0.000004		*
KS.2	18	4	8.837955	-1.162045	12.324089	0.000004		*
MC.10	221	4	8.648716	-1.351284	12.702569	0.000003		*
JN.1.40	26	4	8.488168	-1.511832	13.023663	0.000002		*
LZ.1	28	4	8.453281	-1.546719	13.093438	0.000002		*
LF.7.1	165	5	8.288343	8.288343	-6.576686	0.044601	*	*
NY.7	36	4	8.201967	-1.798033	13.596067	0.000002		*

|||||

XEC.14 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.14	193	9	259.682855	NaN	NaN	NaN	*	*	*
XEC.2	921	8	246.626219	226.626219	-151.252439	5.135572e-14		*
XEC.2.2	273	9	239.494751	209.494751	-116.989503	1.866914e-21		*
XEC.4	192	9	238.969849	225.256251	-148.512501	1.304985e-14		*
KP.3.3	1715	9	238.613194	220.342798	-138.685596	9.620984e-17		*
XEC.28	39	9	237.386239	223.672640	-145.345279	2.687943e-15		*
XEC.8	592	9	235.830690	222.105196	-142.210393	5.592137e-16		*
XEC.29	135	9	231.851981	218.138382	-134.276764	1.060719e-17		*
XEC.17	13	9	230.815307	217.101708	-132.203415	3.749159e-18		*
MC.24.1	25	9	227.862520	213.494994	-124.989989	1.019301e-19		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1150_C|T, 1288_C|T, 1973_C|T, 2060_G|A, 2650_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10156_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11752_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13554_C|T, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20544_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23609_C|T, 23854_C|A, 23948_G|T, 24353_A|G, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): IGS-10285-CVDP-BA12F5F9-8A6C-421B-9AED-9577268198D2



Target: 5350 samples       Number of changes: 147                                                 
BC: NY.13 + XEC.2          BC BR: 6-7                     BC BR coord: 2060 - 2061         
Direction L1: <<           Initial region span: 1-5,10-147 Gap history (edge excluded): 5-10
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  -                                                                             
Rec. model vs L1: 1.09e-149 Rec. model vs L2: 1.10e-09                                             
Flags: Model_2BP_Bad_L1_opp

NY.13 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
NY.13	463	5	10.744395	NaN	NaN	NaN	*	*	*
JV.2	16	3	8.889772	-34.957105	93.914210	8.555135e-18
BN.1	1200	3	7.896973	-22.103027	68.206055	3.257699e-12
XEC.6	45	8	6.741873	5.660779	12.678441	3.724751e+00	*
BA.4.2	1792	3	4.163430	-29.734487	83.468974	1.582137e-15
BF.7	11554	3	2.993263	-20.472019	64.944038	1.671023e-11
JN.1.4	8971	3	2.546824	-10.304045	44.608090	4.340961e-07
XFH.1	10	5	2.405006	-7.594994	39.189988	6.524149e-06		*
BA.4.1	18821	3	1.813614	-32.083089	88.166179	1.508871e-16
BA.5.2.1	73935	3	1.543024	-18.419704	60.839408	1.298034e-10

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	10	245.529961	NaN	NaN	NaN	*	*	*
KP.3.3	1715	6	230.169448	228.439843	-154.879686	2.830180e-04	*
XEC.9	305	6	221.357549	215.071148	-128.142295	4.418724e-10
XEC.8	592	6	220.878384	214.603878	-127.207755	2.775556e-10
XEC.2.1	265	27	220.181434	202.118986	-102.237973	1.049986e-15
MC.24.1	25	15	217.769997	208.234144	-114.468289	4.752193e-13
XEC.32	42	15	215.862282	206.326429	-110.652859	7.037066e-14
XEC.33	169	15	214.739782	205.167781	-108.335561	2.217081e-14
XEC.2.2	273	10	214.497112	205.578206	-109.156412	3.340737e-14		*
XEC.39	155	15	214.238891	204.670248	-107.340496	1.344727e-14

Target sequence

, 241_C|T, 310_A|G, 670_T|G, 897_C|A, 949_A|G, 2060_G|A, 2790_C|T, 3037_C|T, 3411_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5144_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10567_T|C, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22181_C|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24023_C|T, 24378_C|T, 24424_A|T, 24469_T|A, 24784_C|T, 24863_C|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T,
25584_C|T, 25931_C|A, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): IGS-10285-CVDP-C9583D6A-0A9C-425E-AAB8-A1943D5F1208



Target: 5350 samples      Number of changes: 140                                                       
BC: XEC.18 + XEK.1        BC BR: 129-130                    BC BR coord: 28290 - 28291          
Direction L1: >>          Initial region span: 1-129,132-140 Gap history (edge excluded): 129-132
Alt. candidates: [], []                                                                                       
Model 1BP/2BP comparison: 1BP vs 2BP: 2.42e-02                                                                
Rec. model vs L1: 2.87e-09 Rec. model vs L2: 1.98e-54                                                   
Flags: Model_1BP_Best

XEC.18 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.18	165	129	270.753531	NaN	NaN	NaN	*	*	*
XEC.4	192	129	264.623005	264.623005	-253.246010	2.176581e-03	*	*
XEC.6	45	129	263.978329	263.978329	-251.956657	1.141970e-03	*	*
XEC.33	169	129	261.535429	261.535429	-247.070857	9.903869e-05	*	*
XEC.8	592	129	259.416998	259.416998	-242.833996	1.188777e-05	*	*
XEC.24	11	129	259.075313	259.075313	-242.150626	8.461365e-06		*
XEC.36	30	129	258.291226	258.291226	-240.582452	3.859395e-06		*
XEC.17	13	129	257.101994	257.101994	-238.203988	1.174110e-06		*
XEC.15	127	129	256.804479	256.804479	-237.608957	8.741621e-07		*
XEC.2	921	129	255.308199	255.308199	-234.616398	1.960296e-07		*

|||||

XEK.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEK.1	88	132	16.314988	NaN	NaN	NaN	*	*	*
XEC.4	192	132	15.867486	-4.892340	33.784679	6.408243e-01	*	*
KP.3.3.4	292	132	14.421916	-6.337910	36.675820	1.503183e-01	*	*
KP.3.3	1715	132	14.148719	-6.611107	37.222213	1.147499e-01	*	*
KP.1.1.2	12	137	10.631340	-17.877607	59.755215	1.463031e-06
NY.1	25	137	9.810029	-18.516597	61.033194	7.753122e-07
JN.1.11.1	226	132	9.410985	-11.348840	46.697680	1.002759e-03	*	*
MU.2.1	37	137	9.348718	-18.977908	61.955816	4.870008e-07
JN.1.22	516	137	9.181984	-19.257350	62.514701	3.699123e-07
KP.3	769	132	8.888332	-11.871494	47.742987	5.961609e-04	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T,
10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17304_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T,
18894_C|T, 19716_C|T, 19891_G|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25897_A|G, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28303_28311, 28314_G|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28905_C|T, 28958_C|A, 29510_A|C, 29734_29759

 Case 72 (XEC): IGS-10285-CVDP-D4306C2B-0C5B-4513-BF63-848147D0A912



Target: 5350 samples       Number of changes: 146                                                       
BC: XEC.32 + KP.3.3.4      BC BR: 136-137                    BC BR coord: 28361 - 28362          
Direction L1: >>           Initial region span: 1-136,139-146 Gap history (edge excluded): 136-139
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 1.05e-12 Rec. model vs L2: 3.23e-71                                                   
Flags: Model_2BP_Bad_L1_opp

XEC.32 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.32	42	136	247.693106	NaN	NaN	NaN	*	*	*
XEC.9	305	137	240.633597	240.169535	-190.339069	5.394287e-04	*	*
XEC.4	192	143	240.615726	228.122891	-166.245783	3.168524e-09
XEC.8	592	136	237.364079	237.364079	-184.728157	3.263909e-05	*	*
XEC.18	165	136	235.303136	235.303136	-180.606272	4.159981e-06		*
XEC.31	66	136	228.539778	228.539778	-167.079557	4.798320e-09		*
XEC.33	169	136	227.175551	227.175551	-164.351103	1.225398e-09		*
XEC.14	193	143	226.991046	225.558160	-161.116320	2.437203e-10
XEC.3	29	136	225.214395	225.214395	-160.428790	1.726077e-10		*
XEC.24	11	136	221.567155	221.567155	-153.134310	4.486268e-12		*

|||||

KP.3.3.4 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.3.4	292	139	14.531099	NaN	NaN	NaN	*	*	*
KP.3.3	1715	139	13.328665	-6.671335	35.342671	1.645304e-05	*	*
JN.1.30	57	143	12.916045	-15.429459	52.858917	2.581230e-09
JN.1.23	10	143	11.386342	-16.959161	55.918323	5.589283e-10
KP.3.1.10	51	143	10.010592	-4.002922	30.005843	2.363965e-04	*
JN.1.4.7	159	143	8.813068	-19.532435	61.064870	4.277788e-11
XEC.11.1.1	12	139	8.450744	-11.549256	45.098513	1.249940e-07		*
KP.1.1	593	143	8.437611	-9.428045	40.856089	1.041342e-06
JN.2	574	143	8.231969	0.230623	21.538754	1.632594e-02	*
XBB.1.33	27	144	8.163116	-30.182387	82.364775	1.013872e-15

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6664_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12412_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18086_C|A, 18163_A|G,
18492_A|G, 18657_C|T, 18861_A|T, 18888_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22030_G|A, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23600_T|C, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28657_C|T, 28708_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29137_C|T, 29510_A|C, 29734_29759

 Case 72 (XEC): IGS-10285-CVDP-336E7E7C-A753-4F02-8767-9C96D4FFF043



Target: 5350 samples       Number of changes: 145                                               
BC: KP.2.3.13 + XEC.14     BC BR: 5-6                    BC BR coord: 1297 - 1298        
Direction L1: <<           Initial region span: 1-5,9-145 Gap history (edge excluded): 5-9
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 9.57e-156 Rec. model vs L2: 1.49e-23                                           
Flags: Model_2BP_Bad_L1_opp

KP.2.3.13 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3.13	25	5	11.399879	NaN	NaN	NaN	*	*	*
XEC.4.3	10	4	10.581513	0.581513	8.836974	0.000020	*	*
KP.3.3.10	55	4	9.569912	-0.430088	10.860176	0.000007		*
JN.1.34	83	4	8.927300	-1.072700	12.145400	0.000004		*
KS.2	18	4	8.837955	-1.162045	12.324089	0.000004		*
MC.10	221	4	8.648716	-1.351284	12.702569	0.000003		*
JN.1.40	26	4	8.488168	-1.511832	13.023663	0.000002		*
LZ.1	28	4	8.453281	-1.546719	13.093438	0.000002		*
LF.7.1	165	5	8.288343	8.288343	-6.576686	0.044601	*	*
NY.7	36	4	8.201967	-1.798033	13.596067	0.000002		*

|||||

XEC.14 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.14	193	9	269.682855	NaN	NaN	NaN	*	*	*
XEC.2	921	8	256.626219	236.626219	-173.252439	5.135572e-14		*
XEC.2.2	273	9	249.494751	219.494751	-138.989503	1.866914e-21		*
XEC.4	192	9	248.969849	235.256251	-170.512501	1.304985e-14		*
KP.3.3	1715	9	248.613194	230.342798	-160.685596	9.620984e-17		*
XEC.28	39	9	247.386239	233.672640	-167.345279	2.687943e-15		*
XEC.8	592	9	245.830690	232.105196	-164.210393	5.592137e-16		*
XEC.29	135	9	241.851981	228.138382	-156.276764	1.060719e-17		*
XEC.17	13	9	240.815307	227.101708	-154.203415	3.749159e-18		*
MC.24.1	25	9	237.862520	223.494994	-146.989989	1.019301e-19		*

Target sequence

 Case 72 (XEC): IGS-10285-CVDP-F81870C3-13A3-4CE6-8567-7BF50276D37D



Target: 5350 samples      Number of changes: 146                                                 
BC: XEC.39 + XEC.2        BC BR: 12-13                   BC BR coord: 4387 - 4388         
Direction L1: <<          Initial region span: 1-8,13-146 Gap history (edge excluded): 8-13
Alt. candidates: [], []                                                                                 
Model 1BP/2BP comparison: 1BP vs 2BP: 1.32e-01                                                          
Rec. model vs L1: 3.76e-31 Rec. model vs L2: 3.57e-24                                             
Flags: Model_1BP_Best

XEC.39 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.39	155	8	18.622173	NaN	NaN	NaN	*	*	*
XEC.3	29	7	15.661018	1.434276	21.131448	0.000002		*
XEC.22	23	7	15.661018	1.469367	21.061265	0.000002		*
XEC.29	135	7	15.661018	1.447007	21.105987	0.000002		*
XEC.32	42	7	15.661018	1.469367	21.061265	0.000002		*
XEC.36	30	7	15.661018	1.435466	21.129068	0.000002		*
XEC.24	11	7	15.661018	1.469367	21.061265	0.000002		*
XEC.4.1.4	23	7	15.661018	1.469367	21.061265	0.000002		*
XEC.4.3	10	7	15.661018	1.469367	21.061265	0.000002		*
XEC.4.7	13	7	15.661018	1.207003	21.585994	0.000002		*

|||||

XEC.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.2	921	13	231.720443	NaN	NaN	NaN	*	*	*
XEC.9	305	1	215.469140	200.609909	-115.219817	3.083889e-14
XEC.2.1	265	39	210.621889	193.991464	-101.982929	4.112152e-17
XEC.8	592	10	208.733786	202.964998	-119.929996	3.249841e-13
XEC.14	193	10	208.133859	202.341176	-118.682351	1.739515e-13
XEC.33	169	39	202.459161	187.760543	-89.521085	8.098686e-20
XEC.39	155	1	200.249560	185.851827	-85.703654	1.199257e-20
XEC.31	66	39	199.956377	193.039581	-100.079161	1.590338e-17
XEC.40	52	39	199.465110	186.222970	-86.445940	1.744908e-20
XEC.29	135	39	198.105556	177.176990	-68.353981	2.048366e-24

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3511_C|T, 3535_C|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9220_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12525_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14206_C|T, 14408_C|T, 15714_C|T, 15756_T|A,
16293_C|T, 16326_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19545_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26801_C|T, 26833_C|T, 26858_C|T, 26957_T|A, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28065_28119, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 78 (XFC): OZ288079



Target: 72 samples        Number of changes: 143                                                                          
BC: XFC.1 + JN.1.9 + XFC.1 BC BR: 123-124, 140-141                   BC BR coord: 26872 - 26873, 29498 - 29499      
Direction L1: >>          Initial region span: 1-123,124-138,141-143 Gap history (edge excluded): 123-141 -> 138-141
Alt. candidates: [], []                                                                                                          
Model 1BP/2BP comparison: 2BP vs 1BP: 8.19e-03                                                                                   
Rec. model vs L1: 3.78e-25 Rec. model vs L2: 4.97e-148                                                                     
Flags: Model_2BP_Best

XFC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	123	226.595979	NaN	NaN	NaN	*	*	*
LP.8.1	1124	133	180.106630	168.259560	-40.519120	4.116353e-29
XFC.1.1.1	21	111	173.892135	179.881954	-63.763909	4.581572e-24
LP.8.1.1	2345	133	167.966380	157.231562	-18.463125	6.671823e-34
NY.7	36	111	153.828652	144.876281	6.247438	2.874327e-39
NY.15	216	111	135.213296	128.662254	38.675493	2.608862e-46
NY.12	62	111	128.271821	119.529942	56.940116	2.827109e-50
NY.9	107	133	127.448928	116.332387	63.335226	1.152392e-51
PR.2	20	111	126.547589	117.862869	60.274263	5.348626e-51
NY.6	30	111	124.698817	115.813838	64.372325	6.885549e-52

|||||

JN.1.9 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.9	576	138	21.191121	NaN	NaN	NaN	*	*	*
KP.2.1	47	133	17.010073	-8.393355	56.786711	1.041697e-10
JN.1	17255	140	16.555710	16.555710	6.888579	7.134913e+00	*
KP.2.3	4440	138	15.797610	-4.202390	48.404780	6.912047e-09		*
JN.1.4	8971	138	15.601325	-4.398675	48.797350	5.659105e-09		*
KP.3.2.3	759	133	15.452380	-10.046251	60.092501	2.000578e-11
MC.30	104	133	15.421587	-10.084658	60.169316	1.922134e-11
LP.8.1.4	191	133	14.888470	-10.573660	61.147320	1.177550e-11
KP.3.3.1	211	132	14.633121	-20.508222	81.016445	5.705106e-16
XEC.30	135	132	14.125068	-20.985133	81.970266	3.547920e-16

|||||

XFC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	141	7.024671	None	None	None	*	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1683_T|C, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21595_C|T, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A,
22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A,
23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25227_C|T, 25584_C|T, 25695_T|C, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A,
29146_A|T, 29494_G|A, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): OZ288142



Target: 72 samples        Number of changes: 141                                                                    
BC: XFC.1 + JN.1.9 + XFC.1 BC BR: 122-123, 138-139                   BC BR coord: 26872 - 26873, 29498 - 29499
Direction L1: >>          Initial region span: 1-122,123-138,139-141 Gap history (edge excluded): 122-139 ->  
Alt. candidates: [], []                                                                                                    
Model 1BP/2BP comparison: 2BP vs 1BP: 4.61e-03                                                                             
Rec. model vs L1: 3.78e-25 Rec. model vs L2: 2.11e-135                                                               
Flags: Model_2BP_Best

XFC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	122	236.595979	NaN	NaN	NaN	*	*	*
LP.8.1.1	2345	132	183.270866	172.536049	-51.072098	1.343312e-31
LP.8.1	1124	132	182.941714	171.094644	-48.189287	3.182678e-32
XFC.1.1.1	21	122	182.754099	189.881954	-85.763909	4.581572e-24		*
NY.7	36	122	162.662445	154.876281	-15.752562	2.874327e-39		*
NY.15	216	127	143.731958	138.662254	16.675493	2.608862e-46
NY.9	107	132	137.448928	126.332387	41.335226	1.152392e-51
NY.12	62	122	137.329094	129.529942	34.940116	2.827109e-50		*
PR.2	20	122	135.572072	127.862869	38.274263	5.348626e-51		*
NY.6	30	122	133.560781	125.813838	42.372325	6.885549e-52		*

|||||

JN.1.9 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.9	576	138	24.592399	NaN	NaN	NaN	*	*	*
KP.2.1	47	132	17.010073	1.606645	34.786711	1.041697e-10
JN.1	17255	138	16.519214	16.519214	4.961572	3.127833e-04	*	*
KP.2.3	4440	137	15.797610	5.797610	26.404780	6.912047e-09		*
JN.1.4	8971	137	15.601325	5.601325	26.797350	5.659105e-09		*
KP.3.2.3	759	132	15.452380	-0.046251	38.092501	2.000578e-11
MC.30	104	132	15.421587	-0.084658	38.169316	1.922134e-11
LP.8.1.4	191	132	14.888470	-0.573660	39.147320	1.177550e-11
KP.3.3.1	211	131	14.633121	-10.508222	59.016445	5.705106e-16
XEC.30	135	131	14.125068	-10.985133	59.970266	3.547920e-16

|||||

XFC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	139	7.024671	None	None	None	*	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1683_T|C, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11650_C|T, 11727_G|A, 11902_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C,
22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T,
22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T,
26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29494_G|A,
29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/CA-LACPHL-AY11434/2025



Target: 72 samples         Number of changes: 148                                               
BC: LP.8.1 + XFC.1         BC BR: 6-7                    BC BR coord: 1956 - 1957        
Direction L1: <<           Initial region span: 1-6,8-148 Gap history (edge excluded): 6-8
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 9.62e-40 Rec. model vs L2: 4.69e-12                                           
Flags: Model_2BP_Bad_L1_opp

LP.8.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LP.8.1	1124	6	13.756682	NaN	NaN	NaN	*	*	*
JN.1.47	202	4	11.496264	-8.503736	33.007471	2.150824e-10
JN.1.7.1	120	4	10.442759	-9.557241	35.114482	7.526544e-11
JN.1.14	45	4	10.017007	-9.982993	35.965986	4.896086e-11
LB.1.3.2	390	5	9.838643	-0.161357	16.322714	9.052995e-07		*
KP.2.3	4440	4	5.440081	4.213069	7.573863	7.191685e-05	*
BQ.1.1.57	173	3	5.088486	-28.363835	72.727671	5.099369e-19
KP.3.1.1	12013	4	4.452614	1.591607	12.816785	5.209639e-06
BA.5.1.21	324	3	4.442390	-15.017612	46.035225	3.185490e-13
BA.4.1.5	35	3	3.521913	-26.478087	68.956174	3.358625e-18

|||||

XFC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	8	307.914399	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	8	285.600524	275.600524	-241.201048	2.035723e-10		*
LP.8.1	1124	1	256.731388	242.974706	-175.949412	1.379943e-24
NY.7	36	8	245.458851	235.458851	-160.917702	7.518620e-28		*
LP.8.1.1	2345	8	231.968814	221.968814	-133.937628	1.041131e-33		*
PF.2	56	10	213.675881	199.317445	-88.634890	1.508565e-43
NY.7.1	28	8	212.868359	202.868359	-95.736718	5.278141e-42		*
NY.15	216	8	210.634010	200.634010	-91.268021	5.647195e-43		*
PR.2	20	6	209.786515	203.281867	-96.563733	7.953196e-42
JN.1.16.1	466	8	204.128479	202.080282	-94.160564	2.395457e-42		*

Target sequence

, 241_C|T, 670_T|G, 694_T|A, 897_C|A, 1426_C|T, 1954_G|A, 2110_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 8937_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12704_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T,
25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/CA-LACPHL-AY11873/2025



Target: 72 samples        Number of changes: 151                                               
BC: XFC.1 + JN.1.9        BC BR: 132-133                    BC BR coord: 26872 - 26873  
Direction L1: >>          Initial region span: 1-132,133-151 Gap history (edge excluded):
Alt. candidates: [], []                                                                               
Model 1BP/2BP comparison: 1BP vs 2BP: 1.28e-02                                                        
Rec. model vs L1: 1.50e-16 Rec. model vs L2: 3.09e-140                                          
Flags: Model_1BP_Best

XFC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	132	250.752171	NaN	NaN	NaN	*	*	*
LP.8.1	1124	143	239.082446	226.566437	-163.132874	3.137530e-11
XFC.1.1.1	21	132	227.087220	227.087220	-164.174440	5.277413e-11		*
NY.7	36	132	204.682589	204.682589	-119.365177	9.867899e-21		*
LP.8.1.1	2345	143	194.716254	182.970924	-75.941848	3.660328e-30
NY.15	216	137	177.743799	171.060354	-52.120708	2.460780e-35
NY.12	62	132	171.805098	171.805098	-53.610196	5.183488e-35		*
NY.7.1	28	132	171.016159	171.016159	-52.032318	2.352499e-35		*
PF.2	56	132	167.980703	167.980703	-45.961405	1.130956e-36		*
NY.3	209	132	166.385269	166.385269	-42.770539	2.294806e-37		*

|||||

JN.1.9 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.9	576	133	23.325594	NaN	NaN	NaN	*	*	*
JN.1.4	8971	133	16.560932	16.560932	4.878136	1.153447e-03	*	*
JN.1	17255	133	16.052407	16.052407	5.895186	6.926401e-04	*	*
JN.1.18.6	29	134	15.159394	5.159394	27.681211	1.291340e-08		*
MC.2	396	134	12.659426	2.659426	32.681148	1.059997e-09		*
MC.25	26	139	12.601213	-1.983858	41.967715	1.018607e-11
XFC.1	51	145	12.287468	-5.763569	49.527138	2.324735e-13
LB.1.2.2	175	134	11.479504	1.479504	35.040992	3.257145e-10		*
NW.1	111	139	11.314438	-3.270632	44.541265	2.817982e-12
KP.2.3	4440	134	10.600542	9.539073	18.921855	1.030981e-06		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3885_C|T, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9360_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20759_C|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C,
21711_C|T, 21765_21770, 21786_G|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T,
25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/CA-LACPHL-AY11904/2025



Target: 72 samples        Number of changes: 152                                               
BC: XFC.1 + JN.1.9        BC BR: 133-134                    BC BR coord: 26872 - 26873  
Direction L1: >>          Initial region span: 1-133,134-152 Gap history (edge excluded):
Alt. candidates: [], []                                                                               
Model 1BP/2BP comparison: 1BP vs 2BP: 1.28e-02                                                        
Rec. model vs L1: 1.49e-16 Rec. model vs L2: 5.56e-147                                          
Flags: Model_1BP_Best

XFC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	133	254.881633	NaN	NaN	NaN	*	*	*
LP.8.1	1124	144	242.650511	230.134503	-170.269005	1.792186e-11
XFC.1.1.1	21	133	232.103985	232.103985	-174.207971	1.285118e-10		*
NY.7	36	133	207.214447	207.214447	-124.428895	1.992294e-21		*
LP.8.1.1	2345	144	198.522629	186.777300	-83.554599	2.644687e-30
PP.1	127	133	175.774250	175.774250	-61.548500	4.417077e-35		*
NY.7.1	28	133	173.799332	173.799332	-57.598665	6.129195e-36		*
PF.2	56	133	171.169341	171.169341	-52.338682	4.417829e-37		*
NY.3	209	133	170.559510	170.559510	-51.119020	2.400431e-37		*
NY.15	216	138	169.625723	162.942278	-35.884557	1.177512e-40

|||||

JN.1.9 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.9	576	134	23.325594	NaN	NaN	NaN	*	*	*
JN.1.4	8971	134	16.560932	16.560932	4.878136	1.153447e-03	*	*
JN.1	17255	134	16.052407	16.052407	5.895186	6.926401e-04	*	*
JN.1.18.6	29	135	15.159394	5.159394	27.681211	1.291340e-08		*
MC.2	396	135	12.659426	2.659426	32.681148	1.059997e-09		*
MC.25	26	140	12.601213	-1.983858	41.967715	1.018607e-11
XFC.1	51	146	12.287468	-5.763569	49.527138	2.324735e-13
LB.1.2.2	175	135	11.479504	1.479504	35.040992	3.257145e-10		*
NW.1	111	140	11.314438	-3.270632	44.541265	2.817982e-12
KP.2.3	4440	135	10.600542	9.539073	18.921855	1.030981e-06		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3885_C|T, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 13381_C|T,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20759_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21786_G|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T,
24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/CA-LACPHL-AY12024/2025



Target: 72 samples        Number of changes: 151                                               
BC: XFC.1 + JN.1.9        BC BR: 132-133                    BC BR coord: 26872 - 26873  
Direction L1: >>          Initial region span: 1-132,133-151 Gap history (edge excluded):
Alt. candidates: [], []                                                                               
Model 1BP/2BP comparison: 1BP vs 2BP: 1.28e-02                                                        
Rec. model vs L1: 1.49e-16 Rec. model vs L2: 1.11e-146                                          
Flags: Model_1BP_Best

XFC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	132	264.881633	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	132	242.103985	242.103985	-196.207971	1.285118e-10		*
LP.8.1	1124	143	229.483631	216.967622	-145.935245	1.559378e-21
NY.7	36	132	217.214447	217.214447	-146.428895	1.992294e-21		*
LP.8.1.1	2345	143	208.522629	196.777300	-105.554599	2.644687e-30
NY.7.1	28	132	183.799332	183.799332	-79.598665	6.129195e-36		*
PF.2	56	132	181.169341	181.169341	-74.338682	4.417829e-37		*
NY.15	216	137	179.625723	172.942278	-57.884557	1.177512e-40
LP.8.1.6	76	132	174.290113	174.290113	-60.580226	4.542165e-40		*
PR.2	20	132	173.010444	173.010444	-58.020888	1.262891e-40		*

|||||

JN.1.9 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.9	576	133	23.325594	NaN	NaN	NaN	*	*	*
JN.1.4	8971	133	16.560932	16.560932	4.878136	1.153447e-03	*	*
JN.1	17255	133	16.052407	16.052407	5.895186	6.926401e-04	*	*
JN.1.18.6	29	134	15.159394	5.159394	27.681211	1.291340e-08		*
MC.2	396	134	12.659426	2.659426	32.681148	1.059997e-09		*
MC.25	26	139	12.601213	-1.983858	41.967715	1.018607e-11
XFC.1	51	145	12.287468	-5.763569	49.527138	2.324735e-13
LB.1.2.2	175	134	11.479504	1.479504	35.040992	3.257145e-10		*
NW.1	111	139	11.314438	-3.270632	44.541265	2.817982e-12
KP.2.3	4440	134	10.600542	9.539073	18.921855	1.030981e-06		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12565_G|T, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 17427_G|A, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T,
25207_C|T, 25487_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/CA-LACPHL-AY12139/2025



Target: 72 samples        Number of changes: 151                                                   
BC: NY.3 + XFC.1          BC BR: 17-18                    BC BR coord: 6743 - 6744          
Direction L1: <<          Initial region span: 1-14,18-151 Gap history (edge excluded): 14-18
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 4.50e-09                                                            
Rec. model vs L1: 6.67e-86 Rec. model vs L2: 9.60e-22                                               
Flags: Model_1BP_Best

NY.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
NY.3	209	14	39.222924	NaN	NaN	NaN	*	*	*
NY.9	107	14	30.172358	0.172358	35.655285	1.565861e-11		*
NY.7	36	14	27.114003	-2.885997	41.771995	7.378764e-13		*
PD.2	21	14	27.114003	-2.885997	41.771995	7.378764e-13		*
LP.8.1.14	51	14	27.074397	-2.925603	41.851205	7.089439e-13		*
NY.3.1	24	14	27.071443	-2.928557	41.857114	7.054080e-13		*
PP.2	22	14	27.067483	-2.932517	41.865035	7.018898e-13		*
NY.16.1	20	14	27.062709	-2.937291	41.874581	7.018898e-13		*
PF.1	19	14	27.059935	-2.940065	41.880129	6.983891e-13		*
LP.8.1.11	75	14	27.046705	-2.953295	41.906590	6.879914e-13		*

|||||

XFC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	18	256.902897	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	18	240.907031	240.907031	-195.814062	1.125352e-07		*
LP.8.1	1124	18	237.256975	237.256975	-188.513949	2.924916e-09		*
LP.8.1.1	2345	1	190.222440	181.975222	-77.950443	2.872860e-33
NY.7	36	18	187.141818	187.141818	-88.283636	5.028581e-31		*
NY.15	216	18	161.864834	161.864834	-37.729668	5.304598e-42		*
NY.3	209	1	161.759841	136.711223	12.577555	6.309207e-53
NY.9	107	2	156.772363	146.800473	-7.600946	1.520569e-48
PF.2	56	18	155.801181	155.801181	-25.602363	1.232130e-44		*
NY.7.1	28	18	154.300011	154.300011	-22.600022	2.749253e-45		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3885_C|T, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 6742_G|T, 7113_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20759_C|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C,
21711_C|T, 21765_21770, 21786_G|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T,
25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/CA-LACPHL-AY12211/2025



Target: 72 samples        Number of changes: 148                                               
BC: XFC.1 + JN.1.9        BC BR: 129-130                    BC BR coord: 26872 - 26873  
Direction L1: >>          Initial region span: 1-129,130-148 Gap history (edge excluded):
Alt. candidates: [], []                                                                               
Model 1BP/2BP comparison: 1BP vs 2BP: 1.28e-02                                                        
Rec. model vs L1: 1.50e-16 Rec. model vs L2: 4.36e-152                                          
Flags: Model_1BP_Best

XFC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	129	280.752171	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	129	257.087220	257.087220	-234.174440	5.277413e-11		*
LP.8.1	1124	140	245.915566	233.399557	-186.799114	2.729960e-21
NY.7	36	129	234.682589	234.682589	-189.365177	9.867899e-21		*
LP.8.1.1	2345	140	224.716254	212.970924	-145.941848	3.660328e-30
NY.7.1	28	129	201.016159	201.016159	-122.032318	2.352499e-35		*
PF.2	56	129	197.980703	197.980703	-115.961405	1.130956e-36		*
NY.15	216	134	195.359263	188.675819	-97.351637	1.028811e-40
PP.1	127	129	191.414854	191.414854	-102.829708	1.593318e-39		*
LP.8.1.6	76	129	191.406857	191.406857	-102.813713	1.577464e-39		*

|||||

JN.1.9 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.9	576	130	23.325594	NaN	NaN	NaN	*	*	*
JN.1.4	8971	130	16.560932	16.560932	4.878136	1.153447e-03	*	*
JN.1	17255	130	16.052407	16.052407	5.895186	6.926401e-04	*	*
JN.1.18.6	29	131	15.159394	5.159394	27.681211	1.291340e-08		*
MC.2	396	131	12.659426	2.659426	32.681148	1.059997e-09		*
MC.25	26	136	12.601213	-1.983858	41.967715	1.018607e-11
XFC.1	51	142	12.287468	-5.763569	49.527138	2.324735e-13
LB.1.2.2	175	131	11.479504	1.479504	35.040992	3.257145e-10		*
NW.1	111	136	11.314438	-3.270632	44.541265	2.817982e-12
KP.2.3	4440	131	10.600542	9.539073	18.921855	1.030981e-06		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7093_C|T, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/CA-LACPHL-AY12402/2025



Target: 72 samples        Number of changes: 154                                               
BC: XFC.1 + JN.1.9        BC BR: 135-136                    BC BR coord: 26872 - 26873  
Direction L1: >>          Initial region span: 1-135,136-154 Gap history (edge excluded):
Alt. candidates: [], []                                                                               
Model 1BP/2BP comparison: 1BP vs 2BP: 1.28e-02                                                        
Rec. model vs L1: 1.50e-16 Rec. model vs L2: 3.04e-152                                          
Flags: Model_1BP_Best

XFC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	135	257.836990	NaN	NaN	NaN	*	*	*
LP.8.1	1124	146	222.952890	210.436882	-128.873763	2.596818e-21
XFC.1.1.1	21	135	219.890700	219.890700	-147.781400	3.316621e-17		*
LP.8.1.1	2345	146	212.278179	200.532850	-109.065699	1.302945e-25
NY.7	36	135	211.010518	211.010518	-130.021037	4.614885e-21		*
NY.7.1	28	135	177.779578	177.779578	-63.559157	1.708265e-35		*
PF.2	56	135	175.216726	175.216726	-58.433453	1.313983e-36		*
NY.15	216	140	172.644387	165.960942	-39.921884	1.256593e-40
LP.8.1.6	76	135	167.978050	167.978050	-43.956100	9.472603e-40		*
PP.1	127	135	167.503055	167.503055	-43.006111	5.890870e-40		*

|||||

JN.1.9 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.9	576	136	23.325594	NaN	NaN	NaN	*	*	*
JN.1.4	8971	136	16.560932	16.560932	4.878136	1.153447e-03	*	*
JN.1	17255	136	16.052407	16.052407	5.895186	6.926401e-04	*	*
JN.1.18.6	29	137	15.159394	5.159394	27.681211	1.291340e-08		*
MC.2	396	137	12.659426	2.659426	32.681148	1.059997e-09		*
MC.25	26	142	12.601213	-1.983858	41.967715	1.018607e-11
XFC.1	51	148	12.287468	-5.763569	49.527138	2.324735e-13
LB.1.2.2	175	137	11.479504	1.479504	35.040992	3.257145e-10		*
NW.1	111	142	11.314438	-3.270632	44.541265	2.817982e-12
KP.2.3	4440	137	10.600542	9.539073	18.921855	1.030981e-06		*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1148_G|T, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T,
7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11200_C|T, 11288_11296, 11727_G|A, 12493_C|T, 12789_C|T, 12815_C|T,
12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G,
22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G,
24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 25997_T|C, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T,
29734_29759

 Case 78 (XFC): USA/CA-LACPHL-AY12567/2025



Target: 72 samples        Number of changes: 155                                                                          
BC: XFC.1 + JN.1.7 + XFC.1 BC BR: 134-135, 152-153                   BC BR coord: 26872 - 26873, 29509 - 29510      
Direction L1: >>          Initial region span: 1-134,136-152,153-155 Gap history (edge excluded): 134-153 -> 134-136
Alt. candidates: [], []                                                                                                          
Model 1BP/2BP comparison: 2BP vs 1BP: 5.56e-02                                                                                   
Rec. model vs L1: 2.68e-23 Rec. model vs L2: 7.82e-130                                                                     
Flags: Model_2BP_Best

XFC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	134	243.755002	NaN	NaN	NaN	*	*	*
LP.8.1	1124	146	219.764580	207.490506	-116.981013	1.582675e-19
XFC.1.1.1	21	134	219.367917	226.495772	-154.991544	2.838955e-11		*
LP.8.1.1	2345	142	216.986475	207.776614	-117.553227	2.104582e-19
NY.7	36	134	197.435890	189.649726	-81.299451	2.828644e-27		*
LP.8.1.4	191	142	170.525280	149.406347	-0.812693	9.405825e-45
NY.7.1	28	134	164.513251	156.621727	-15.243453	1.278885e-41		*
PF.2	56	134	160.985318	153.069696	-8.139392	3.673552e-43		*
NY.15	216	139	158.567301	153.497596	-8.995192	5.647195e-43
PP.1	127	134	154.603936	146.847255	4.305491	7.271149e-46		*

|||||

JN.1.7 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.7	1974	136	19.702918	NaN	NaN	NaN	*	*	*
JN.1	17255	135	13.585285	13.585285	14.829430	4.842422e+01	*	*
LP.8.1.6	76	148	8.749941	-19.153460	80.306919	2.925912e-13
KP.3.1.1	12013	136	8.046951	7.781907	26.436187	1.458758e-01	*	*
JN.1.4	8971	135	7.369652	7.369652	27.260695	9.681048e-02	*	*
KP.2.3	4440	136	7.361657	6.300188	29.399625	3.320682e-02	*	*
MC.25	26	144	5.827046	-14.380015	70.760030	3.467507e-11
KQ.1	383	141	5.623898	-8.966401	59.932802	7.793311e-09
BA.2.56	900	152	5.434323	-22.843164	87.686328	7.306588e-15
FL.17	35	152	4.955677	-59.223042	160.446084	1.158994e-30

|||||

XFC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	153	7.024671	None	None	None	*	*	*

Target sequence

, 241_C|T, 670_T|G, 888_C|T, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3231_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T, 7217_T|C,
7842_A|G, 8293_C|T, 8393_G|A, 8525_G|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 17733_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G,
22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G,
24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 27879_C|T, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29020_A|G, 29510_A|C,
29625_C|T, 29734_29759

 Case 78 (XFC): USA/CA-LACPHL-AY12730/2025



Target: 72 samples        Number of changes: 150                                               
BC: XFC.1 + JN.1.9        BC BR: 130-131                    BC BR coord: 26872 - 26873  
Direction L1: >>          Initial region span: 1-130,131-150 Gap history (edge excluded):
Alt. candidates: [], []                                                                               
Model 1BP/2BP comparison: 1BP vs 2BP: 4.15e-07                                                        
Rec. model vs L1: 8.89e-23 Rec. model vs L2: 2.22e-152                                          
Flags: Model_1BP_Best

XFC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	130	282.179410	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	130	257.610003	257.610003	-233.220007	2.134935e-11		*
LP.8.1	1124	141	247.027765	234.511757	-187.023513	1.982358e-21
NY.7	36	130	235.764988	235.764988	-189.529975	6.953791e-21		*
LP.8.1.1	2345	141	226.152937	214.407607	-146.815215	3.697115e-30
NY.7.1	28	130	201.944408	201.944408	-121.888815	1.426863e-35		*
PF.2	56	130	199.468567	199.468567	-116.937134	1.200890e-36		*
NY.15	216	135	196.789969	190.106524	-98.213049	1.028811e-40
LP.8.1.6	76	130	192.435188	192.435188	-102.870377	1.057406e-39		*
PP.1	127	130	192.389265	192.389265	-102.778529	1.010877e-39		*

|||||

JN.1.9 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.9	576	131	23.660979	NaN	NaN	NaN	*	*	*
JN.1.4	8971	131	17.171097	17.171097	11.657806	1.518549e-03	*	*
JN.1	17255	131	16.760803	16.760803	12.478394	1.007785e-03	*	*
MC.25	26	137	15.341461	0.756391	44.487218	1.128457e-10
KB.1	86	147	12.770066	-37.806556	121.613113	2.023437e-27
XDD.1	18	147	12.743619	-37.890161	121.780323	1.858552e-27
KB.2	24	147	12.738800	-37.971354	121.942707	1.715659e-27
EG.5.1.7	91	147	12.718438	-37.938227	121.876454	1.767909e-27
XDK.1	127	143	12.695712	-5.360527	56.721055	2.493298e-13
MC.2	396	132	12.676357	2.676357	40.647286	7.697156e-10		*

Target sequence

, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7093_C|T, 7113_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T,
25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759, 29762_C|T

 Case 78 (XFC): USA/CA-LACPHL-AY13055/2025



Target: 72 samples         Number of changes: 157                                                   
BC: LP.8.1.1 + XFC.1       BC BR: 20-21                    BC BR coord: 6694 - 6695          
Direction L1: <<           Initial region span: 1-18,21-157 Gap history (edge excluded): 18-21
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  -                                                                               
Rec. model vs L1: 1.86e-43 Rec. model vs L2: 7.06e-27                                               
Flags: Model_2BP_Bad_L1_opp

LP.8.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LP.8.1.1	2345	18	19.397030	NaN	NaN	NaN	*	*	*
NY.1	25	18	12.872101	-7.127899	62.255799	1.907285e-08		*
MC.9.1	15	5	11.845534	-64.450330	176.900660	2.435880e-33
KP.3.2.1	70	5	10.542015	-62.988183	173.976366	1.048880e-32
XFJ.1	59	5	10.441274	-69.874613	187.749226	1.073021e-35
KP.3.3.1	211	5	9.348011	-56.616285	161.232570	6.156773e-30
MC.11	393	6	9.345400	-36.584475	121.168951	3.078021e-21
LP.8.1	1124	18	8.501551	-11.498449	70.996899	2.412952e-10		*
MC.24	831	5	8.467215	-57.510213	163.020427	2.515704e-30
NY.13	463	18	8.443691	-11.556309	71.112619	2.283823e-10		*

|||||

XFC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	21	239.769652	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	21	210.907031	210.907031	-125.814062	2.911319e-13		*
LP.8.1	1124	10	209.727890	203.969557	-111.939114	2.833072e-16
LP.8.1.1	2345	3	204.363168	185.153775	-74.307550	1.909883e-24
NY.7	36	10	176.142054	170.356880	-44.713759	7.135896e-31
NY.15	216	68	150.831708	143.288136	9.423727	1.256806e-42
KP.3.1	1957	20	144.723143	144.391837	7.216325	3.775655e-42		*
LP.8.1.4	191	68	144.587112	127.025122	41.949757	1.085097e-49
PF.2	56	12	144.359085	139.673023	16.653954	3.382936e-44
NY.6	30	68	142.922302	131.807138	32.385724	1.292398e-47

Target sequence

, 44_C|T, 174_G|C, 241_C|T, 670_T|G, 897_C|A, 1426_C|T, 1954_G|A, 2066_A|G, 2644_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A,
6694_G|A, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10729_A|G, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T,
12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 14955_A|G, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22005_A|C, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G,
22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26305_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C,
29625_C|T, 29734_29759

 Case 78 (XFC): USA/CA-LACPHL-AY13072/2025



Target: 72 samples        Number of changes: 151                                               
BC: XFC.1 + JN.1.9        BC BR: 131-132                    BC BR coord: 26872 - 26873  
Direction L1: >>          Initial region span: 1-131,132-151 Gap history (edge excluded):
Alt. candidates: [], []                                                                               
Model 1BP/2BP comparison: 1BP vs 2BP: 1.56e-01                                                        
Rec. model vs L1: 1.78e-22 Rec. model vs L2: 1.47e-145                                          
Flags: Model_1BP_Best

XFC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	131	260.752171	NaN	NaN	NaN	*	*	*
LP.8.1	1124	143	244.675505	232.322274	-178.644547	4.497880e-13
XFC.1.1.1	21	131	237.087220	237.087220	-188.174440	5.277413e-11		*
LP.8.1.1	2345	143	222.245284	212.091270	-138.182540	7.365980e-22
NY.7	36	131	214.682589	214.682589	-143.365177	9.867899e-21		*
NY.7.1	28	131	181.016159	181.016159	-76.032318	2.352499e-35		*
LP.8.1.4	191	143	178.008479	161.478630	-36.957261	7.719458e-44
PF.2	56	131	177.980703	177.980703	-69.961405	1.130956e-36		*
NY.15	216	136	175.359263	168.675819	-51.351637	1.028811e-40
PP.1	127	131	171.414854	171.414854	-56.829708	1.593318e-39		*

|||||

JN.1.9 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.9	576	132	23.138211	NaN	NaN	NaN	*	*	*
JN.1.4	8971	132	14.726517	14.726517	16.546966	2.215195e-04	*	*
JN.1	17255	132	14.544716	14.544716	16.910568	1.850286e-04	*	*
XFC.1	51	145	12.287468	-15.763569	77.527138	1.269911e-17
KP.2.3	4440	133	10.450298	9.388829	27.222341	1.067704e-06		*
KP.1.1.1	578	132	9.369149	9.369149	27.261702	1.046562e-06		*
JN.1.18.6	29	145	8.988265	-4.840606	55.681211	7.054080e-13
XDD.1.1	29	145	8.953173	-43.277945	132.555891	1.426135e-29
LE.1	27	145	8.890020	-19.131163	84.262326	4.389067e-19
JN.1.39.3	31	145	8.889973	-19.013427	84.026855	4.923978e-19

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16600_T|C, 16726_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24734_C|T, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T,
25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C,
27807_C|T, 27810_T|C, 27881_C|T, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/IVY-G25Z05G8/2025



Target: 72 samples        Number of changes: 146                                                                          
BC: XFC.1 + MC.25 + XFC.1 BC BR: 132-133, 139-140                   BC BR coord: 27387 - 27388, 28880 - 28881      
Direction L1: >>          Initial region span: 1-132,134-139,140-146 Gap history (edge excluded): 132-140 -> 132-134
Alt. candidates: [], []                                                                                                          
Model 1BP/2BP comparison: 2BP vs 1BP: 5.04e-01                                                                                   
Rec. model vs L1: 4.85e-09 Rec. model vs L2: 1.36e-215                                                                     
Flags: Model_2BP_Best

XFC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	132	284.875629	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	132	260.282175	272.672827	-241.345654	2.312747e-11		*
LP.8.1	1124	138	245.437741	243.118748	-182.237496	3.377184e-24
NY.7	36	132	238.350148	235.826781	-167.653562	2.292854e-27		*
LP.8.1.1	2345	138	213.022632	211.772332	-119.544663	8.192618e-38
NY.7.1	28	132	205.427510	202.798782	-101.597564	1.041840e-41		*
PF.2	56	132	201.935614	199.282788	-94.565576	3.099246e-43		*
PP.1	127	132	195.518195	193.024310	-82.048620	5.923422e-46		*
LP.8.1.6	76	132	195.512826	193.045739	-82.091478	6.043083e-46		*
NY.15	216	132	192.807395	199.683932	-95.367864	4.623532e-43		*

|||||

MC.25 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.25	26	134	14.942259	NaN	NaN	NaN	*	*	*
NW.1	111	134	13.769894	3.769894	8.460211	0.310367	*	*
JN.1.47.2	60	134	11.507160	1.507160	12.985680	0.032225	*	*
JN.1.18.4	64	134	10.735366	0.735366	14.529267	0.014921	*	*
GW.1	11	136	10.468938	-8.767402	33.534804	0.000001
MC.2	396	133	9.723046	9.723046	-3.446092	119.701363	*	*
JN.1.9	576	133	9.638327	9.638327	-3.276654	109.947172	*	*
LB.1.2	199	134	9.602673	-0.397327	16.794654	0.004820	*	*
KQ.1	383	134	8.926897	-1.073103	18.146206	0.002442	*	*
JN.1.8.1	1498	133	8.846168	2.917321	10.165359	0.131994	*	*

|||||

XFC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	140	12.287468	None	None	None	*	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21983_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26115_A|G,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T,
28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/MA-MASPHL-14198/2025



Target: 72 samples        Number of changes: 148                                                   
BC: JN.1.16.1 + XFC.1     BC BR: 13-14                    BC BR coord: 4809 - 4810          
Direction L1: <<          Initial region span: 1-13,16-148 Gap history (edge excluded): 13-16
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 9.12e-04                                                            
Rec. model vs L1: 9.33e-65 Rec. model vs L2: 3.02e-23                                               
Flags: Model_1BP_Best

JN.1.16.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.16.1	466	13	24.093307	NaN	NaN	NaN	*	*	*
JN.1.16	332	12	23.686312	13.686312	0.627376	3.012967e-05	*	*
JN.1	17255	12	18.420777	18.229291	-8.458583	2.837023e-03	*	*
XEC.30	135	12	18.413069	8.413069	11.173862	1.549753e-07		*
KP.1.1.3	979	15	16.112732	8.429205	11.141590	1.573175e-07
XDY.6	11	13	13.873495	13.873495	0.253010	3.643430e-05	*	*
MC.1	932	15	13.492808	10.433837	7.132326	1.168254e-06
XDY.5	17	13	12.640378	12.640378	2.719244	1.059636e-05	*	*
JN.1.28	51	13	12.510761	12.510761	2.978479	9.304615e-06		*
KP.2.3.11	56	13	12.136337	12.136337	3.727325	6.394962e-06		*

|||||

XFC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	16	292.619810	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	16	277.511247	265.928095	-227.856189	1.888629e-10		*
LP.8.1	1124	7	252.608827	242.690934	-181.381868	1.524554e-20
LP.8.1.1	2345	7	222.698112	211.916205	-119.832410	6.572493e-34
NY.7	36	16	221.261127	216.963714	-129.927428	1.025457e-31		*
PF.2	56	16	201.018142	196.720729	-89.441458	1.654343e-40		*
JN.1.16.1	466	1	197.521316	173.428008	-42.856017	1.270302e-50
NY.15	216	7	195.669971	182.152816	-60.305632	7.818552e-47
NY.9	107	7	190.349048	178.773337	-53.546674	2.662018e-48
LF.7	58	22	189.359284	143.224339	17.551322	9.683718e-64

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1393_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4579_T|A, 4999_C|T, 5979_C|T, 6183_A|G, 6255_C|T, 7113_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
13728_T|C, 14408_C|T, 15714_C|T, 15720_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24990_C|T,
25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/MA-MASPHL-14204/2025



Target: 72 samples        Number of changes: 146                                                            
BC: XFC.1 + NY.9 + XFC.1  BC BR: 11-12, 13-14                   BC BR coord: 4581 - 4582, 6182 - 6183
Direction L1: <<          Initial region span: 1-11,12-13,14-146 Gap history (edge excluded): 11-14 ->
Alt. candidates: [], []                                                                                            
Model 1BP/2BP comparison: 2BP vs 1BP: 6.21e-06                                                                     
Rec. model vs L1: 4.10e-16 Rec. model vs L2: 7.41e-96                                                        
Flags: Model_2BP_Best

XFC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	11	6.256999	None	None	None	*	*	*

|||||

NY.9 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
NY.9	107	12	9.901323	NaN	NaN	NaN	*	*	*
PP.1	127	12	8.631353	8.631353	-11.262706	2.808316e-01	*	*
KP.1.1.3	979	12	7.683526	7.683526	-9.367053	1.091535e-01	*	*
B.1.1.232	220	13	7.642016	-2.357984	10.715968	4.737505e-06		*
LP.8.1	1124	12	6.447326	6.447326	-6.894652	3.158730e-02	*	*
MC.1.4	125	12	5.764823	5.764823	-5.529645	1.600267e-02	*	*
LP.8.1.1	2345	12	5.714219	5.714219	-5.428438	1.522221e-02	*	*
FL.32.1	13	13	5.208004	-9.242033	24.484065	4.870837e-09		*
NP.1	16	13	5.000364	-4.999636	15.999271	3.380743e-07		*
JN.1.7.3	19	13	4.828514	-5.171486	16.342972	2.852214e-07		*

|||||

XFC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	14	297.332378	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	14	278.094463	272.515666	-235.031333	3.193736e-14		*
LP.8.1	1124	5	252.615939	240.847899	-171.695797	5.654109e-28
LP.8.1.1	2345	5	222.727067	211.686359	-113.372718	1.219455e-40
NY.7	36	14	221.844343	216.314337	-122.628673	1.250112e-38		*
PF.2	56	14	201.868421	196.209946	-82.419892	2.319843e-47		*
NY.15	216	5	195.665339	194.653577	-79.307154	4.899261e-48
NY.9	107	5	190.219291	175.018008	-40.036015	1.454650e-56
NY.7.1	28	14	189.326586	183.760212	-57.520424	9.088500e-53		*
JN.1.16.1	466	14	185.066418	187.560672	-65.121345	4.062667e-51		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1393_A|G, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 4579_T|A, 4999_C|T, 5979_C|T, 6183_A|G, 6255_C|T, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 13728_T|C, 14408_C|T,
15714_C|T, 15720_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T,
25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/MA-MASPHL-14213/2025



Target: 72 samples        Number of changes: 148                                                   
BC: JN.1.16.1 + XFC.1     BC BR: 13-14                    BC BR coord: 4809 - 4810          
Direction L1: <<          Initial region span: 1-13,16-148 Gap history (edge excluded): 13-16
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 9.12e-04                                                            
Rec. model vs L1: 2.29e-69 Rec. model vs L2: 3.02e-23                                               
Flags: Model_1BP_Best

JN.1.16.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.16.1	466	13	24.093307	NaN	NaN	NaN	*	*	*
JN.1.16	332	12	23.686312	13.686312	0.627376	3.012967e-05	*	*
JN.1	17255	12	18.420777	18.229291	-8.458583	2.837023e-03	*	*
XEC.30	135	12	18.413069	8.413069	11.173862	1.549753e-07		*
KP.1.1.3	979	15	16.112732	8.429205	11.141590	1.573175e-07
XDY.6	11	13	13.873495	13.873495	0.253010	3.643430e-05	*	*
MC.1	932	15	13.492808	10.433837	7.132326	1.168254e-06
XDY.5	17	13	12.640378	12.640378	2.719244	1.059636e-05	*	*
JN.1.28	51	13	12.510761	12.510761	2.978479	9.304615e-06		*
KP.2.3.11	56	13	12.136337	12.136337	3.727325	6.394962e-06		*

|||||

XFC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	16	296.521338	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	16	280.525472	268.942319	-247.884639	7.717080e-11		*
LP.8.1	1124	7	257.068190	247.150297	-204.300593	2.655683e-20
LP.8.1.1	2345	7	226.921874	216.139967	-142.279933	9.051162e-34
NY.7	36	16	226.760258	222.462845	-154.925690	5.053787e-31		*
PF.2	56	16	205.860494	201.563081	-113.126162	4.235086e-40		*
NY.15	216	7	199.434502	185.917346	-81.834693	6.763222e-47
NY.9	107	7	195.820098	184.244387	-78.488774	1.273157e-47
NY.7.1	28	16	193.918452	189.621039	-89.242077	2.749253e-45		*
JN.1.16.1	466	1	192.243379	168.150072	-46.300144	1.302903e-54

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1393_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4579_T|A, 4999_C|T, 5979_C|T, 6183_A|G, 6255_C|T, 7113_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
13728_T|C, 14408_C|T, 15714_C|T, 15720_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T,
25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/MN-MDH-46633/2025



Target: 72 samples         Number of changes: 147                                               
BC: XEC.28 + XFC.1         BC BR: 4-5                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-4,6-147 Gap history (edge excluded): 4-6
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 1.64e-198 Rec. model vs L2: 2.95e-08                                           
Flags: Model_2BP_Bad_L1_opp

XEC.28 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.28	39	4	9.397373	NaN	NaN	NaN	*	*	*
KP.1.1.2	12	4	8.575206	8.575206	-9.150412	0.440432	*	*
JN.1.39.1	40	4	8.469846	8.469846	-8.939691	0.396531	*	*
LF.7.1	165	5	8.237031	5.923623	-3.847246	0.031117	*	*
PY.2	17	4	8.226899	8.226899	-8.453799	0.310367	*	*
MC.30.1	18	4	8.169741	8.169741	-8.339482	0.293758	*	*
XEC.4.6	10	4	8.141342	8.141342	-8.282683	0.285076	*	*
MD.1	19	4	8.115674	8.115674	-8.231348	0.278037	*	*
JN.1.8.2	17	4	8.105650	8.105650	-8.211300	0.275271	*	*
PG.6	23	4	7.924619	7.924619	-7.849237	0.229925	*	*

|||||

XFC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	6	313.272614	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	6	289.474465	269.067637	-222.135273	1.396231e-15		*
LP.8.1	1124	1	265.075276	259.980734	-203.961467	1.574782e-19
NY.7	36	6	252.290303	242.290303	-168.580605	3.270025e-27		*
LP.8.1.1	2345	1	242.865382	238.001179	-160.002359	4.481544e-29
NY.7.1	28	6	220.192287	202.884840	-89.769680	2.518703e-44		*
NY.15	216	6	216.138195	206.138195	-96.276390	6.528381e-43		*
PF.2	56	6	215.707064	205.707064	-95.414128	4.225590e-43		*
NY.13	463	3	209.653135	205.000295	-94.000589	2.087900e-43
PR.2	20	6	206.605116	196.605116	-77.210232	4.718540e-47		*

Target sequence

, 241_C|T, 516_518, 670_T|G, 897_C|A, 1426_C|T, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
8937_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12704_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T,
25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/MN-MDH-46650/2025



Target: 72 samples        Number of changes: 147                                                                          
BC: XFC.1 + MC.25 + XFC.1 BC BR: 133-134, 140-141                   BC BR coord: 27387 - 27388, 28880 - 28881      
Direction L1: >>          Initial region span: 1-133,135-140,141-147 Gap history (edge excluded): 133-141 -> 133-135
Alt. candidates: [], []                                                                                                          
Model 1BP/2BP comparison: 2BP vs 1BP: 5.04e-01                                                                                   
Rec. model vs L1: 4.82e-09 Rec. model vs L2: 1.67e-215                                                                     
Flags: Model_2BP_Best

XFC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	133	299.169932	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	133	274.782847	287.173498	-272.346997	2.853185e-11		*
LP.8.1	1124	139	259.918781	257.599788	-213.199577	4.083858e-24
NY.7	36	133	252.850819	250.327452	-198.654904	2.828644e-27		*
LP.8.1.1	2345	139	227.499306	226.249006	-150.498012	9.906920e-38
NY.7.1	28	133	219.928181	217.299453	-132.598906	1.285296e-41		*
PF.2	56	133	216.400248	213.747422	-125.494845	3.673552e-43		*
PP.1	127	133	210.018866	207.524981	-113.049962	7.307595e-46		*
LP.8.1.6	76	133	210.013497	207.546410	-113.092820	7.455219e-46		*
NY.15	216	133	207.298786	214.175323	-126.350645	5.647195e-43		*

|||||

MC.25 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.25	26	135	14.942259	NaN	NaN	NaN	*	*	*
NW.1	111	135	13.769894	3.769894	8.460211	0.310367	*	*
JN.1.47.2	60	135	11.507160	1.507160	12.985680	0.032225	*	*
JN.1.18.4	64	135	10.735366	0.735366	14.529267	0.014921	*	*
GW.1	11	137	10.468938	-8.767402	33.534804	0.000001
MC.2	396	134	9.723046	9.723046	-3.446092	119.701363	*	*
JN.1.9	576	134	9.638327	9.638327	-3.276654	109.947172	*	*
LB.1.2	199	135	9.602673	-0.397327	16.794654	0.004820	*	*
KQ.1	383	135	8.926897	-1.073103	18.146206	0.002442	*	*
JN.1.8.1	1498	134	8.846168	2.917321	10.165359	0.131994	*	*

|||||

XFC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	141	12.287468	None	None	None	*	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T,
26115_A|G, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/MN-MDH-46834/2025



Target: 72 samples        Number of changes: 145                                               
BC: LP.8.1 + XFC.1        BC BR: 7-8                    BC BR coord: 3037 - 3038        
Direction L1: <<          Initial region span: 1-7,9-145 Gap history (edge excluded): 7-9
Alt. candidates: [], []                                                                               
Model 1BP/2BP comparison: 1BP vs 2BP: 3.83e-01                                                        
Rec. model vs L1: 3.15e-39 Rec. model vs L2: 2.04e-06                                           
Flags: Model_1BP_Best

LP.8.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LP.8.1	1124	7	12.711222	NaN	NaN	NaN	*	*	*
NY.13	463	7	12.469276	12.469276	-6.938552	7.866279e-01	*	*
LP.8.1.1	2345	7	11.983068	11.983068	-5.966137	4.843246e-01	*	*
XEL.4	10	4	11.039560	2.120654	13.758691	2.516642e-05	*
XEC.8	592	4	9.570849	-5.622564	29.245127	1.089458e-08
KP.2.2.1	55	4	8.749548	-0.169358	18.338716	2.548514e-06
JN.1.1.3	30	4	8.331510	-7.831918	33.663837	1.201134e-09
MC.33	31	4	8.298720	-0.620186	19.240371	1.625004e-06
XEC.29	135	4	7.520580	-7.684727	33.369454	1.388558e-09
XEC.32	42	4	7.301891	-7.903416	33.806833	1.114344e-09

|||||

XFC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	9	325.706674	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	14	302.806169	291.783361	-281.566723	4.089554e-11
LP.8.1	1124	1	274.660019	261.948797	-221.897593	4.513362e-24
NY.7	36	9	264.599199	254.599199	-207.198399	2.900252e-27		*
LP.8.1.1	2345	1	242.577555	230.594486	-159.188972	1.089423e-37
PF.2	56	9	233.491859	218.052328	-134.104657	3.881257e-43		*
NY.7.1	28	9	232.501184	222.501184	-143.002367	3.323402e-41		*
NY.15	216	9	228.494494	218.494494	-134.988988	6.056663e-43		*
NY.13	463	1	219.657701	207.188425	-112.376849	7.456488e-48
PR.2	20	9	219.019373	209.019373	-116.038746	4.648290e-47		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1426_C|T, 1954_G|A, 2790_C|T, 3037_C|T, 3218_3220, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T,
25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/MN-MDH-46650/2025



Target: 72 samples        Number of changes: 147                                                                          
BC: XFC.1 + MC.25 + XFC.1 BC BR: 133-134, 140-141                   BC BR coord: 27387 - 27388, 28880 - 28881      
Direction L1: >>          Initial region span: 1-133,135-140,141-147 Gap history (edge excluded): 133-141 -> 133-135
Alt. candidates: [], []                                                                                                          
Model 1BP/2BP comparison: 2BP vs 1BP: 5.04e-01                                                                                   
Rec. model vs L1: 4.82e-09 Rec. model vs L2: 1.67e-215                                                                     
Flags: Model_2BP_Best

XFC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	133	299.169932	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	133	274.782847	287.173498	-272.346997	2.853185e-11		*
LP.8.1	1124	139	259.918781	257.599788	-213.199577	4.083858e-24
NY.7	36	133	252.850819	250.327452	-198.654904	2.828644e-27		*
LP.8.1.1	2345	139	227.499306	226.249006	-150.498012	9.906920e-38
NY.7.1	28	133	219.928181	217.299453	-132.598906	1.285296e-41		*
PF.2	56	133	216.400248	213.747422	-125.494845	3.673552e-43		*
PP.1	127	133	210.018866	207.524981	-113.049962	7.307595e-46		*
LP.8.1.6	76	133	210.013497	207.546410	-113.092820	7.455219e-46		*
NY.15	216	133	207.298786	214.175323	-126.350645	5.647195e-43		*

|||||

MC.25 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.25	26	135	14.942259	NaN	NaN	NaN	*	*	*
NW.1	111	135	13.769894	3.769894	8.460211	0.310367	*	*
JN.1.47.2	60	135	11.507160	1.507160	12.985680	0.032225	*	*
JN.1.18.4	64	135	10.735366	0.735366	14.529267	0.014921	*	*
GW.1	11	137	10.468938	-8.767402	33.534804	0.000001
MC.2	396	134	9.723046	9.723046	-3.446092	119.701363	*	*
JN.1.9	576	134	9.638327	9.638327	-3.276654	109.947172	*	*
LB.1.2	199	135	9.602673	-0.397327	16.794654	0.004820	*	*
KQ.1	383	135	8.926897	-1.073103	18.146206	0.002442	*	*
JN.1.8.1	1498	134	8.846168	2.917321	10.165359	0.131994	*	*

|||||

XFC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	141	12.287468	None	None	None	*	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T,
26115_A|G, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/MN-MDH-46650/2025



Target: 72 samples        Number of changes: 147                                                                          
BC: XFC.1 + MC.25 + XFC.1 BC BR: 133-134, 140-141                   BC BR coord: 27387 - 27388, 28880 - 28881      
Direction L1: >>          Initial region span: 1-133,135-140,141-147 Gap history (edge excluded): 133-141 -> 133-135
Alt. candidates: [], []                                                                                                          
Model 1BP/2BP comparison: 2BP vs 1BP: 5.04e-01                                                                                   
Rec. model vs L1: 4.82e-09 Rec. model vs L2: 1.67e-215                                                                     
Flags: Model_2BP_Best

XFC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	133	299.169932	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	133	274.782847	287.173498	-272.346997	2.853185e-11		*
LP.8.1	1124	139	259.918781	257.599788	-213.199577	4.083858e-24
NY.7	36	133	252.850819	250.327452	-198.654904	2.828644e-27		*
LP.8.1.1	2345	139	227.499306	226.249006	-150.498012	9.906920e-38
NY.7.1	28	133	219.928181	217.299453	-132.598906	1.285296e-41		*
PF.2	56	133	216.400248	213.747422	-125.494845	3.673552e-43		*
PP.1	127	133	210.018866	207.524981	-113.049962	7.307595e-46		*
LP.8.1.6	76	133	210.013497	207.546410	-113.092820	7.455219e-46		*
NY.15	216	133	207.298786	214.175323	-126.350645	5.647195e-43		*

|||||

MC.25 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.25	26	135	14.942259	NaN	NaN	NaN	*	*	*
NW.1	111	135	13.769894	3.769894	8.460211	0.310367	*	*
JN.1.47.2	60	135	11.507160	1.507160	12.985680	0.032225	*	*
JN.1.18.4	64	135	10.735366	0.735366	14.529267	0.014921	*	*
GW.1	11	137	10.468938	-8.767402	33.534804	0.000001
MC.2	396	134	9.723046	9.723046	-3.446092	119.701363	*	*
JN.1.9	576	134	9.638327	9.638327	-3.276654	109.947172	*	*
LB.1.2	199	135	9.602673	-0.397327	16.794654	0.004820	*	*
KQ.1	383	135	8.926897	-1.073103	18.146206	0.002442	*	*
JN.1.8.1	1498	134	8.846168	2.917321	10.165359	0.131994	*	*

|||||

XFC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	141	12.287468	None	None	None	*	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T,
26115_A|G, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/MN-MDH-47236/2025



Target: 72 samples        Number of changes: 150                                                   
BC: LP.8.1 + XFC.1        BC BR: 13-14                    BC BR coord: 4809 - 4810          
Direction L1: <<          Initial region span: 1-12,14-150 Gap history (edge excluded): 12-14
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 1.40e-01                                                            
Rec. model vs L1: 1.97e-30 Rec. model vs L2: 9.11e-21                                               
Flags: Model_1BP_Best

LP.8.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LP.8.1	1124	12	21.462790	NaN	NaN	NaN	*	*	*
KP.2.3	4440	13	20.034250	20.034250	-10.068499	5.271130e+03	*	*
LP.8.1.4	191	12	14.197412	4.197412	21.605175	6.961120e-04	*	*
LP.8.1.3	77	12	13.807079	3.807079	22.385841	4.713074e-04	*	*
JN.1	17255	13	12.815379	12.815379	4.369242	3.857426e+00	*	*
KP.3.1.1	12013	13	12.582727	12.582727	4.834546	3.064854e+00	*	*
NW.1.2	34	10	12.439477	-14.132002	58.264005	7.660070e-12
NY.13	463	12	11.826208	1.826208	26.347584	6.507305e-05	*	*
LP.8.1.1	2345	12	11.339445	1.339445	27.321110	4.006530e-05	*	*
XEL.4	10	4	11.039560	-8.601653	47.203306	1.931440e-09

|||||

XFC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	14	262.472712	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	15	240.052125	238.468972	-166.937945	3.756306e-11		*
LP.8.1	1124	1	239.151328	227.688538	-145.377076	7.817474e-16
LP.8.1.1	2345	6	200.395816	193.389195	-76.778390	9.925805e-31
NY.7	36	6	199.536259	192.462103	-74.924205	3.916263e-31
JN.1.16.1	466	15	194.890507	184.890507	-59.781015	2.019587e-34		*
LF.7	58	21	168.564990	132.430045	45.139911	3.327929e-57
NY.7.1	28	6	167.438243	160.364087	-10.728174	4.510144e-45
NY.6	30	6	164.087870	157.013714	-4.027428	1.582355e-46
NY.16	136	6	163.570184	156.540696	-3.081393	9.840430e-47

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1426_C|T, 1884_C|T, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4483_T|C, 4999_C|T, 6183_A|G, 6255_C|T, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 8937_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12704_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|C,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T,
25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28079_G|T, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29212_G|T, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/MN-MDH-47239/2025



Target: 72 samples        Number of changes: 148                                                                          
BC: XFC.1 + MC.25 + XFC.1 BC BR: 134-135, 141-142                   BC BR coord: 27387 - 27388, 28880 - 28881      
Direction L1: >>          Initial region span: 1-134,136-141,142-148 Gap history (edge excluded): 134-142 -> 134-136
Alt. candidates: [], []                                                                                                          
Model 1BP/2BP comparison: 2BP vs 1BP: 5.04e-01                                                                                   
Rec. model vs L1: 4.82e-09 Rec. model vs L2: 1.67e-215                                                                     
Flags: Model_2BP_Best

XFC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	134	289.169932	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	134	264.782847	277.173498	-250.346997	2.853185e-11		*
LP.8.1	1124	140	249.918781	247.599788	-191.199577	4.083858e-24
NY.7	36	134	242.850819	240.327452	-176.654904	2.828644e-27		*
LP.8.1.1	2345	140	217.499306	216.249006	-128.498012	9.906920e-38
NY.7.1	28	134	209.928181	207.299453	-110.598906	1.285296e-41		*
PF.2	56	134	206.400248	203.747422	-103.494845	3.673552e-43		*
PP.1	127	134	200.018866	197.524981	-91.049962	7.307595e-46		*
LP.8.1.6	76	134	200.013497	197.546410	-91.092820	7.455219e-46		*
NY.15	216	134	197.298786	204.175323	-104.350645	5.647195e-43		*

|||||

MC.25 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.25	26	136	14.942259	NaN	NaN	NaN	*	*	*
NW.1	111	136	13.769894	3.769894	8.460211	0.310367	*	*
JN.1.47.2	60	136	11.507160	1.507160	12.985680	0.032225	*	*
JN.1.18.4	64	136	10.735366	0.735366	14.529267	0.014921	*	*
GW.1	11	138	10.468938	-8.767402	33.534804	0.000001
MC.2	396	135	9.723046	9.723046	-3.446092	119.701363	*	*
JN.1.9	576	135	9.638327	9.638327	-3.276654	109.947172	*	*
LB.1.2	199	136	9.602673	-0.397327	16.794654	0.004820	*	*
KQ.1	383	136	8.926897	-1.073103	18.146206	0.002442	*	*
JN.1.8.1	1498	135	8.846168	2.917321	10.165359	0.131994	*	*

|||||

XFC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	142	12.287468	None	None	None	*	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6324_A|G, 6647_G|A, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T,
25925_C|T, 26060_C|T, 26115_A|G, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/NJ-CDC-LC1136665/2025



Target: 72 samples        Number of changes: 149                                                                          
BC: XFC.1 + MC.2 + XFC.1  BC BR: 134-135, 145-146                   BC BR coord: 27387 - 27388, 28958 - 28959      
Direction L1: >>          Initial region span: 1-134,135-145,147-149 Gap history (edge excluded): 134-147 -> 145-147
Alt. candidates: [], []                                                                                                          
Model 1BP/2BP comparison: 2BP vs 1BP: 3.23e-01                                                                                   
Rec. model vs L1: 1.57e-12 Rec. model vs L2: 3.88e-171                                                                     
Flags: Model_2BP_Best

XFC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	134	289.169932	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	134	264.782847	261.910701	-225.821403	2.838955e-11		*
LP.8.1	1124	140	261.624109	254.402257	-210.804514	1.554558e-14
NY.7	36	134	242.850819	225.064655	-152.129310	2.828644e-27		*
LP.8.1.1	2345	140	227.683641	220.795089	-143.590179	3.954949e-29
NY.7.1	28	134	209.928181	192.036656	-86.073312	1.278885e-41		*
PF.2	56	134	206.400248	188.484626	-78.969251	3.673552e-43		*
PP.1	127	134	200.018866	182.262184	-66.524368	7.271149e-46		*
LP.8.1.6	76	134	200.013497	182.283613	-66.567227	7.455219e-46		*
NY.15	216	134	197.298786	188.912526	-79.825052	5.647195e-43		*

|||||

MC.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.2	396	145	14.983314	NaN	NaN	NaN	*	*	*
JN.1.9	576	145	14.899386	14.899386	-5.798773	0.918512	*	*
JN.1.7	1974	145	13.013784	13.013784	-2.027567	0.139457	*	*
KP.2.3	4440	145	12.963798	12.963798	-1.927596	0.132655	*	*
PY.1	82	138	11.879550	4.692712	14.614576	0.000034	*
JN.1	17255	145	11.321642	11.321642	1.356716	0.025604	*	*
MC.35	258	140	10.969312	6.232109	11.535782	0.000158	*
JN.1.4	8971	145	10.901092	10.901092	2.197816	0.016823	*	*
NC.1.2.2	14	140	10.791292	6.054088	11.891823	0.000132	*
LZ.5	14	140	10.791292	6.054088	11.891823	0.000132	*

|||||

XFC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	147	7.024671	None	None	None	*	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C,
16877_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19290_C|T, 19955_C|T, 20055_A|G, 20438_G|A, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C,
21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G,
22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A,
23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T,
25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29353_C|T, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/NY-PRL-250415_82H03/2025



Target: 72 samples         Number of changes: 149                                               
BC: JN.4 + XFC.1           BC BR: 4-5                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-4,6-149 Gap history (edge excluded): 4-6
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 1.79e-211 Rec. model vs L2: 1.28e-07                                           
Flags: Model_2BP_Bad_L1_opp

JN.4 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.4	91	4	10.251882	NaN	NaN	NaN	*	*	*
JN.1.19	438	4	7.261974	7.261974	-6.523948	5.028744e-02	*	*
XBF.7.1	13	3	7.184143	-2.815857	13.631714	2.118081e-06		*
KP.2.2	1334	4	6.120417	6.120417	-4.240834	1.608288e-02	*	*
BF.7.19	413	3	5.920445	-4.079555	16.159109	5.978057e-07		*
LB.1.7	1971	4	5.758423	5.758423	-3.516847	1.122064e-02	*	*
JN.1	17255	4	4.682442	4.682442	-1.364885	3.810480e-03	*	*
BA.5.1.15	339	3	4.610322	-5.389678	18.779355	1.613000e-07		*
BM.1.1.3	341	3	4.604475	-5.395525	18.791050	1.604955e-07		*
BQ.1.1.2	1102	3	4.350924	-5.649076	19.298152	1.243706e-07		*

|||||

XFC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	6	280.269783	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	18	260.907031	236.786940	-155.573880	2.868463e-15
LP.8.1	1124	6	246.405456	236.405456	-154.810912	1.961631e-15		*
LP.8.1.1	2345	6	225.548928	215.548928	-113.097856	1.719515e-24		*
NY.7	36	6	219.537001	209.537001	-101.074003	4.198795e-27		*
NY.15	216	6	194.198673	184.198673	-50.397345	4.171324e-38		*
NY.7.1	28	6	186.695195	169.387748	-20.775495	1.543024e-44		*
PF.2	56	6	182.702448	172.702448	-27.404896	4.225590e-43		*
NY.9	107	6	179.176877	169.176877	-20.353754	1.244513e-44		*
LP.8.1.4	191	6	177.046346	167.046346	-16.092692	1.478945e-45		*

Target sequence

, 241_C|T, 670_T|G, 674_G|A, 897_C|A, 1825_C|T, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T,
25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

 Case 78 (XFC): USA/NY-PRL-250512_81H01/2025



Target: 72 samples        Number of changes: 149                                               
BC: XFC.1 + JN.1          BC BR: 129-130                    BC BR coord: 26872 - 26873  
Direction L1: >>          Initial region span: 1-129,130-149 Gap history (edge excluded):
Alt. candidates: [], []                                                                               
Model 1BP/2BP comparison: 1BP vs 2BP: 4.63e-03                                                        
Rec. model vs L1: 1.93e-18 Rec. model vs L2: 1.21e-83                                           
Flags: Model_1BP_Best

XFC.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XFC.1	51	129	280.752171	NaN	NaN	NaN	*	*	*
XFC.1.1.1	21	129	257.087220	257.087220	-234.174440	5.277413e-11		*
LP.8.1	1124	140	245.915566	233.399557	-186.799114	2.729960e-21
NY.7	36	129	234.682589	234.682589	-189.365177	9.867899e-21		*
LP.8.1.1	2345	140	224.716254	212.970924	-145.941848	3.660328e-30
NY.7.1	28	129	201.016159	201.016159	-122.032318	2.352499e-35		*
PF.2	56	129	197.980703	197.980703	-115.961405	1.130956e-36		*
NY.15	216	134	195.359263	188.675819	-97.351637	1.028811e-40
PP.1	127	129	191.414854	191.414854	-102.829708	1.593318e-39		*
LP.8.1.6	76	129	191.406857	191.406857	-102.813713	1.577464e-39		*

|||||

JN.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1	17255	130	14.340323	NaN	NaN	NaN	*	*	*
JN.1.9	576	130	13.325594	13.325594	19.348812	3.624024e-01	*	*
KP.3.1.1	12013	131	7.560725	7.295681	31.408638	8.717569e-04	*	*
EG.5.1.13	511	146	7.353268	-43.249112	132.498224	9.749465e-26
LP.8.1.1	2345	131	6.572054	6.148954	33.702093	2.774139e-04	*	*
JN.1.4	8971	130	6.560932	6.560932	32.878136	4.180122e-04	*	*
JG.3	1482	146	6.256479	-44.399894	134.799787	3.087039e-26
LP.1	659	136	6.138066	-8.508009	63.016017	1.192260e-10
BA.2.86.1	1343	142	5.562791	-16.218628	78.437256	5.345159e-14
EG.5.1.1	4177	146	5.218272	-17.978801	81.957601	9.196072e-15

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18303_C|T, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29711_G|T, 29734_29759

 Case 81 (XFM): USA/CT-DPH-1298970001/2025



Target: 4 samples          Number of changes: 151                                               
BC: LF.7.9 + MC.1          BC BR: 141-142                    BC BR coord: 28271 - 28272  
Direction L1: >>           Initial region span: 1-141,142-151 Gap history (edge excluded):
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 3.03e-19 Rec. model vs L2: 1.82e-208                                          
Flags: Model_2BP_Bad_L1_opp

LF.7.9 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7.9	20	141	335.593566	NaN	NaN	NaN	*	*	*
LF.7.6.2	17	121	238.279720	221.159594	-116.319188	2.002216e-50
XFJ.1	59	141	196.032277	196.032277	-66.064553	2.441691e-61		*
XFJ.3	14	141	190.874228	190.874228	-55.748457	1.408973e-63		*
LF.7	58	121	151.037108	134.065403	57.869194	2.996630e-88
LF.7.9.1	48	121	143.116416	117.572463	90.855075	2.055633e-95
LF.7.2.1	67	121	138.660760	121.667790	82.664420	1.240375e-93
LF.7.1	165	123	136.267638	128.473831	69.052338	1.119249e-90
PY.1	82	121	135.288811	102.949113	120.101774	9.195180e-102
PC.3.1	27	121	134.590562	117.470436	91.059127	1.860014e-95

|||||

MC.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.1	932	142	7.683264	NaN	NaN	NaN	*	*	*
JN.1.7.5	427	145	7.201075	-1.269791	28.539582	1.290901e-04	*
LB.1.3	778	145	6.549281	-1.947511	29.895022	6.539923e-05	*
KP.2.3	4440	142	6.376026	6.376026	13.247948	2.698201e-01	*	*
GV.1	137	149	6.069949	-10.751732	47.503464	9.857828e-09
NY.3	209	145	5.453218	-3.037381	32.074762	2.209852e-05	*
KS.1	505	145	5.312971	-3.257166	32.514332	1.773448e-05	*
XEC.4	192	148	5.041013	-12.123325	50.246651	2.492449e-09
JN.1.39	1007	145	4.953672	-3.570287	33.140575	1.294242e-05	*
JN.1.4	8971	142	4.697798	4.697798	16.604405	5.053950e-02	*	*

Target sequence

, 241_C|T, 569_G|A, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4504_G|A, 4579_T|A, 5239_C|T, 6070_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8338_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15207_T|C, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21928_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22884_T|G,
22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T,
25000_C|T, 25207_C|T, 25413_C|T, 25584_C|T, 25844_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26555_A|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27414_G|A, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28660_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29700_A|G, 29711

 Case 81 (XFM): USA/NY-PRL-250422_82C10/2025



Target: 4 samples          Number of changes: 152                                               
BC: LF.7.9 + JN.1.2        BC BR: 141-142                    BC BR coord: 28271 - 28272  
Direction L1: >>           Initial region span: 1-141,142-152 Gap history (edge excluded):
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 2.93e-20 Rec. model vs L2: 1.08e-155                                          
Flags: Model_2BP_Bad_L1_opp

LF.7.9 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7.9	20	141	335.997567	NaN	NaN	NaN	*	*	*
LF.7.6.2	17	120	235.094567	225.422215	-106.844430	9.456190e-49
XFJ.1	59	141	201.101587	201.101587	-58.203174	2.592235e-59		*
XFJ.3	14	141	196.713834	196.713834	-49.427667	3.230674e-61		*
LF.7	58	120	147.547708	137.726937	68.546126	7.767148e-87
LF.7.1	165	137	145.523314	140.666455	62.667090	1.469222e-85
LF.7.9.3	20	120	144.070262	127.448147	89.103707	2.678464e-91
LF.7.9.1	48	120	139.552185	121.413898	101.172203	6.410894e-94
LF.7.2.1	67	120	135.262966	125.463460	93.073081	3.679690e-92
XFG.3	480	81	133.717473	113.857393	116.285215	3.339276e-97

|||||

JN.1.2 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.2	650	142	10.289153	NaN	NaN	NaN	*	*	*
JN.1.7.5	427	145	9.488295	1.017429	19.965142	9.373865e-05	*
MC.13	807	142	9.173604	9.173604	3.652792	3.279153e-01	*	*
LB.1.3	778	145	8.754250	0.257458	21.485083	4.383842e-05	*
KP.3.1.1	12013	142	8.470598	8.470598	5.058804	1.620258e-01	*	*
BA.2.86.1	1343	142	8.370252	8.370252	5.259496	1.466070e-01	*	*
GV.1	137	149	8.196587	-8.625094	39.250188	6.099860e-09
MC.1	932	142	8.017999	8.017999	5.964002	1.033122e-01	*	*
JN.1.1	3081	142	7.872476	7.872476	6.255047	8.892162e-02	*	*
NY.3	209	145	7.737843	-0.752756	23.505512	1.596678e-05	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4504_G|A, 4579_T|A, 5239_C|T, 6070_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 7926_C|T, 8293_C|T, 8338_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15207_T|C, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C,
21711_C|T, 21765_21770, 21928_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T,
25413_C|T, 25584_C|T, 25844_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26555_A|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27414_G|A, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28382_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29700_A|G, 29711, 29734_29759

 Case 90 (XFA): USA/CA-LACPHL-AY11366/2025



Target: 2 samples          Number of changes: 152                                                   
BC: MC.1.1 + XEC.4.1.4     BC BR: 33-34                    BC BR coord: 13341 - 13342        
Direction L1: <<           Initial region span: 1-33,38-152 Gap history (edge excluded): 33-38
Alt. candidates: [], []                                                                                    
Model 1BP/2BP comparison:  1BP vs 2BP: 1.99e-02                                                            
Rec. model vs L1: 1.86e-143 Rec. model vs L2: 1.09e-67                                               
Flags: Model_1BP_Best

MC.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.1.1	107	33	69.885223	NaN	NaN	NaN	*	*	*
KP.3.1.1	12013	34	68.900630	68.897784	-71.795568	3.734392e-01	*	*
MC.24	831	30	67.572119	51.158381	-36.316761	7.376253e-09
KP.2.3	4440	36	56.378437	51.699799	-37.399597	1.265770e-08
MC.10.1	650	31	55.781856	49.360047	-32.720095	1.219286e-09
MC.1.2	49	33	55.396785	55.396785	-44.793571	5.094164e-07		*
MC.5	19	30	55.118385	37.553171	-9.106341	9.104569e-15
MC.11.3	19	30	55.118385	38.651783	-11.303566	2.721522e-14
MC.11.1	26	30	55.118385	38.705850	-11.411700	2.875399e-14
MC.23	64	30	55.086888	38.674353	-11.348707	2.790418e-14

|||||

XEC.4.1.4 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4.1.4	23	38	211.890620	NaN	NaN	NaN	*	*	*
XEC.4.1	68	38	211.515947	206.194585	-158.389170	6.872893e-01	*	*
XEC.4.1.1	12	38	209.689515	204.368153	-154.736307	1.108032e-01	*	*
KP.3.1.1	12013	1	209.009269	140.111485	-26.222969	1.370215e-29
PT.1	10	38	204.583917	193.257299	-132.514598	1.649563e-06		*
KP.3.3	1715	8	188.685496	151.324369	-48.648738	1.017188e-24
XEC.4	192	8	179.701736	164.260081	-74.520162	4.216970e-19
JN.1	17255	1	179.339972	134.971869	-15.943738	8.026295e-32
XEC.8	592	8	174.889014	160.884994	-67.769988	1.442968e-20
KP.3.1	1957	8	166.660686	128.072404	-2.144808	8.088783e-35

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3552_C|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12616_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13121_A|T, 13264_C|T, 13297_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16056_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21255_G|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23584_T|C, 23598_A|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T,
25470_A|T, 25584_C|T, 26060_C|T, 26097_A|G, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27294_C|T, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 27995_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28783_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29353_C|T, 29510_A|C, 29728_29776

 Case 97 (XEV): OZ249780



Target: 57 samples          Number of changes: 137                                                             
BC: XEC.18 + KP.2.3 + XEC.18 BC BR: 5-6, 15-16                   BC BR coord: 896 - 897, 7841 - 7842     
Direction L1: <<            Initial region span: 1-5,7-15,16-137 Gap history (edge excluded): 5-16 -> 5-7
Alt. candidates: [], []                                                                                               
Model 1BP/2BP comparison:   2BP vs 1BP: 7.95e-01                                                                      
Rec. model vs L1: 5.34e-23  Rec. model vs L2: 1.32e-56                                                         
Flags: Model_2BP_Best

XEC.18 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.18	165	5	8.722792	None	None	None	*	*	*

|||||

KP.2.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3	4440	7	21.112612	NaN	NaN	NaN	*	*	*
JN.1	17255	7	12.510614	2.510614	18.978771	1.831876e-04	*	*
KP.3.1.1	12013	6	10.499322	10.499322	3.001356	5.406409e-01	*	*
MC.11.1	26	7	8.460749	-1.539251	27.078501	3.191562e-06		*
MC.10.1.5	19	7	8.460749	-1.539251	27.078501	3.191562e-06		*
KP.3.2.8	26	7	8.460749	-9.077943	42.155886	1.695989e-09		*
MC.10.1.3	10	7	8.460749	-1.539251	27.078501	3.191562e-06		*
MK.2	15	7	8.460749	-1.539251	27.078501	3.191562e-06		*
MC.36.2	24	7	8.460749	-1.539251	27.078501	3.191562e-06		*
MC.30.1	18	7	8.460749	-9.190911	42.381821	1.519325e-09		*

|||||

XEC.18 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.18	165	16	201.704901	NaN	NaN	NaN	*	*	*
XEC.2	921	14	201.361877	205.824638	-123.649275	1.000170e-02	*
XEC.4	192	7	190.709428	197.054908	-106.109816	1.553500e-06
MC.24.1	25	7	188.234502	189.348135	-90.696269	6.999585e-10
XEC.31	66	16	188.115015	196.919675	-105.839350	1.357318e-06		*
XEC.2.2	273	23	187.745352	192.329145	-96.658291	1.378066e-08
KP.3.1.1	12013	1	187.382552	176.883230	-65.766460	2.701417e-15
KP.3.3	1715	7	184.110359	185.010026	-82.020052	9.125029e-12
XEC.30	135	16	182.307800	190.738736	-93.477472	2.810229e-09		*
XEC.14	193	16	179.232730	187.979954	-87.959909	1.778643e-10		*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1684_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4699_T|G, 6183_A|G, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 9693_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12616_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 14925_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21711_C|T, 21738_T|C, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A,
22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T,
22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T,
24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27798_G|T, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28378_G|T, 28770_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 97 (XEV): USA/CA-LACPHL-AY11866/2025



Target: 57 samples         Number of changes: 154                                                 
BC: KP.2.3.12 + KP.3.3     BC BR: 8-9                     BC BR coord: 942 - 943           
Direction L1: <<           Initial region span: 1-8,10-154 Gap history (edge excluded): 8-10
Alt. candidates: [], []                                                                                  
Model 1BP/2BP comparison:  -                                                                             
Rec. model vs L1: 1.22e-135 Rec. model vs L2: 6.04e-09                                             
Flags: Model_2BP_Bad_L1_opp

KP.2.3.12 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3.12	62	8	6.087460	NaN	NaN	NaN	*	*	*
BA.5.1.1	4637	5	4.845359	-6.819697	29.639395	0.000002
NM.1	41	7	2.729300	-7.270700	30.541400	0.000002		*

|||||

KP.3.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.3	1715	10	218.905592	NaN	NaN	NaN	*	*	*
XEC.8	592	10	212.712221	196.437715	-76.875430	3.859395e-06		*
KP.3.1.1	12013	4	209.167576	204.813585	-93.627171	1.673923e-02	*
XEC.2	921	10	203.289361	193.289361	-70.578722	1.653833e-07		*
XEC.32	42	10	198.943693	182.657292	-49.314584	3.978963e-12		*
XEC.18	165	10	196.243094	179.962772	-43.925543	2.700957e-13		*
XEC.2.2	273	43	193.335885	164.785999	-13.571998	6.901245e-20
JN.1	17255	10	192.908348	182.908348	-49.816695	5.134698e-12		*
KP.3.1	1957	10	188.361835	178.361835	-40.723670	5.425941e-14		*
MC.24.1	25	10	182.175940	172.175940	-28.351881	1.117799e-16		*

Target sequence

, 21_C|T, 44_C|T, 135, 241_C|T, 670_T|G, 835_C|T, 897_C|A, 942_G|A, 1684_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11845_T|C, 12616_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14120_C|T,
14408_C|T, 15714_C|T, 15756_T|A, 16877_C|T, 16915_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22113_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22227_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22630_G|T, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G,
22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T,
25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26446_T|C, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28378_G|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29353_C|T, 29510_A|C, 29555_C|T, 29734_29759

 Case 97 (XEV): USA/MN-MDH-46878/2025



Target: 57 samples         Number of changes: 146                                               
BC: MC.11.2 + XEC.18       BC BR: 6-7                    BC BR coord: 2060 - 2061        
Direction L1: <<           Initial region span: 1-4,9-146 Gap history (edge excluded): 4-9
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 1.45e-127 Rec. model vs L2: 1.18e-17                                           
Flags: Model_2BP_Bad_L1_opp

MC.11.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
MC.11.2	146	4	10.588478	NaN	NaN	NaN	*	*	*
MU.2.1.1	10	4	9.006580	-10.993420	33.986841	0.204948	*	*
MC.17	46	4	8.866818	-11.133182	34.266365	0.178173	*	*
KP.2.3.4	70	4	8.506555	-11.493445	34.986889	0.124307	*	*
NH.4	32	4	8.248894	-11.751106	35.502212	0.096328	*	*
KP.2.6.1	49	4	8.110491	-11.889509	35.779017	0.083743	*	*
LF.7.6	15	4	7.907967	-12.092033	36.184066	0.068563	*	*
PH.1	63	4	7.778126	-12.221874	36.443748	0.060205	*	*
PA.1	52	4	7.664742	-12.335258	36.670516	0.053665	*	*
KP.2.28	22	4	7.524975	-12.475025	36.950050	0.046654	*	*

|||||

XEC.18 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.18	165	9	259.750273	NaN	NaN	NaN	*	*	*
XEC.4	192	9	259.326260	239.326260	-178.652519	5.658142e-07		*
MC.24.1	25	9	256.115434	250.016360	-200.032720	2.484745e-02	*	*
XEC.8	592	9	253.563192	244.992634	-189.985269	1.641057e-04	*	*
XEC.32	42	9	250.165396	230.165396	-160.330792	5.950267e-11		*
XEC.9	305	9	248.050341	228.050341	-156.100683	7.178002e-12		*
KP.3.3	1715	9	245.649443	225.649443	-151.298886	6.511737e-13		*
XEC.14	193	9	244.206949	224.206949	-148.413899	1.535116e-13		*
XEK.1	88	15	241.344673	207.363280	-114.726559	7.457998e-21
XEC.31	66	17	241.260839	217.396492	-134.792983	1.692762e-16

Target sequence

, 186_C|T, 241_C|T, 670_T|G, 897_C|A, 1684_C|A, 2032_T|C, 2106_C|T, 2549_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12616_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26645_C|T, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 26879_T|G, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28378_G|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29604_T|C, 29734_29759

 Case 97 (XEV): IGS-10285-CVDP-BE7CCBB1-AFB1-4DBD-B00A-60439A98F4F0



Target: 57 samples         Number of changes: 146                                               
BC: LF.7.7.2 + XEC.4       BC BR: 5-6                    BC BR coord: 896 - 897          
Direction L1: <<           Initial region span: 1-5,7-146 Gap history (edge excluded): 5-7
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 1.46e-246 Rec. model vs L2: 1.10e-13                                           
Flags: Model_2BP_Bad_L1_opp

LF.7.7.2 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7.7.2	239	5	8.442286	NaN	NaN	NaN	*	*	*
JN.1.46	308	5	6.836866	6.836866	-3.673733	0.200890	*	*
JN.1.8.1	1498	5	6.829969	6.829969	-3.659938	0.199888	*	*
BE.1.1.1	737	4	6.627662	-3.372338	16.744677	0.000007		*
JN.1.8	352	5	6.551767	6.551767	-3.103534	0.151072	*	*
MC.2	396	5	6.319967	6.319967	-2.639935	0.120032	*	*
KP.3.1.1	12013	6	6.297777	4.221627	1.556747	0.014699	*	*
BA.5.3.1	660	4	6.175858	-3.824142	17.648285	0.000005		*
KP.1.1.3	979	5	5.992658	5.992658	-1.985317	0.086726	*	*
JN.1.42	494	5	5.871571	5.871571	-1.743141	0.076536	*	*

|||||

XEC.4 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4	192	7	251.070415	NaN	NaN	NaN	*	*	*
XEC.18	165	16	246.224447	223.999714	-143.999429	2.070780e-05	*
KP.3.3	1715	7	245.514843	235.514843	-167.029685	2.075081e+00	*	*
XEC.31	66	16	243.887029	213.736280	-123.472560	7.212755e-10
XEK.1	88	14	243.290433	209.309039	-114.618078	8.636705e-12
XEC.2	921	14	240.250424	222.851307	-141.702613	6.556852e-06
MC.24.1	25	7	236.115434	226.115434	-148.230869	1.716591e-04	*	*
XEC.32	42	7	230.165396	213.878995	-123.757990	8.338230e-10		*
XEC.14	193	16	229.292147	207.064018	-110.128035	9.148649e-13
XEC.24	11	16	227.045082	204.832619	-105.665238	9.837399e-14

Target sequence

, 241_C|T, 337_C|T, 521_523, 670_T|G, 897_C|A, 1684_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5440_A|G, 6183_A|G, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12616_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18457_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23593_G|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25856_A|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28378_G|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

 Case 102 (XEW): USA/2025CV0191/2025



Target: 19 samples         Number of changes: 146                                               
BC: AY.36 + XEC.4          BC BR: 3-4                    BC BR coord: 570 - 571          
Direction L1: <<           Initial region span: 1-3,5-146 Gap history (edge excluded): 3-5
Alt. candidates: [], []                                                                                
Model 1BP/2BP comparison:  -                                                                           
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 3.86e+02                                           
Flags: Model_2BP_Bad_L1_opp

AY.36 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
AY.36	5867	3	4.804577	NaN	NaN	NaN	*	*	*
AY.14	7575	3	4.312293	4.312293	1.375413	0.609571	*	*
XBB.1.5.12	581	4	3.694368	2.612646	4.774707	0.111917	*	*
LP.8.1.1	2345	4	3.683419	2.613291	4.773417	0.111917	*	*
BA.5.2.35	1368	4	3.391462	2.304563	5.390873	0.082085	*	*
BA.4.2	1792	4	3.249850	2.162952	5.674097	0.071361	*	*
KP.3.1	1957	4	3.066618	1.993612	6.012777	0.060205	*	*
B.1.258	3961	3	1.969245	1.969245	6.061510	0.058719	*	*
BA.5.2.20	5259	4	1.791525	0.705578	8.588845	0.016573	*	*
EG.5.1.1	4177	4	1.734324	0.656322	8.687355	0.015764	*	*

|||||

XEC.4 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4	192	5	253.940174	NaN	NaN	NaN	*	*	*
XEC.8	592	5	249.765041	240.967562	-169.935124	1.560756e-02	*	*
KP.3.3	1715	5	240.993675	238.469257	-164.938515	1.281146e-03	*	*
XEC.2	921	5	233.434693	230.894237	-149.788474	6.573824e-07		*
KP.3.1.1	12013	5	222.724692	220.189203	-128.378406	1.474673e-11		*
MC.24.1	25	5	218.688082	216.106804	-120.213609	2.480862e-13		*
XEC.32	42	5	212.649469	203.822612	-95.645225	1.152037e-18		*
XEC.15	127	5	209.861491	201.050507	-90.101014	7.182890e-20		*
XEC.30	135	5	207.355932	198.551661	-85.103323	5.896075e-21		*
XEC.9	305	5	205.593729	196.766872	-81.533745	9.893441e-22		*

Target sequence

, 186_C|T, 241_C|T, 570_A|G, 670_T|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11575_C|T, 11727_G|A, 12616_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13121_A|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18647_C|T, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23595_C|T, 23599_T|G, 23604_C|G, 23638_C|T, 23854_C|A, 23948_G|T, 24376_T|C, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27797_A|G, 27807_C|T, 27810_T|C, 28077_G|T,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C

 Case 122 (XFN): OZ261586



Target: 27 samples         Number of changes: 134                                                       
BC: JN.1.16.1 + KP.3.3.10  BC BR: 116-117                    BC BR coord: 27263 - 27264          
Direction L1: >>           Initial region span: 1-116,118-134 Gap history (edge excluded): 116-118
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 4.61e-19 Rec. model vs L2: 1.60e-29                                                   
Flags: Model_2BP_Bad_L1_opp

JN.1.16.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.16.1	466	116	139.541873	NaN	NaN	NaN	*	*	*
KP.3.3	1715	132	138.573741	132.335787	13.328426	7.428622e-04	*
KP.3	769	116	136.593561	136.593561	4.812877	5.260206e-02	*	*
KP.2.3	4440	123	131.236252	121.004250	35.991499	8.919731e-09
KP.3.1	1957	116	128.702092	128.702092	20.595817	1.959963e-05	*	*
XEC.32	42	132	128.224644	112.014310	53.971380	1.111845e-12
MC.24.1	25	125	126.665191	121.201324	35.597352	1.084025e-08
KP.3.1.1	12013	134	126.256683	122.182326	33.635347	2.888337e-08
XEC.39	155	132	122.125070	115.892137	46.215726	5.357171e-11
KP.2	1589	116	120.642020	120.642020	36.715959	6.192048e-09		*

|||||

KP.3.3.10 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.3.10	55	118	20.410343	NaN	NaN	NaN	*	*	*
XEC.2.2	273	118	17.696525	7.696525	32.606951	6.620495e-02	*	*
XEC.32	42	118	17.530195	7.530195	32.939610	5.613476e-02	*	*
KP.3.1.1	12013	118	14.074357	4.074357	39.851287	1.773146e-03	*	*
LP.8.1	1124	118	13.890711	3.890711	40.218578	1.473669e-03	*	*
JN.1.11.1	226	125	10.949753	0.471441	47.057119	4.820730e-05	*
KR.1.4	24	131	10.910774	-24.624117	97.248234	6.088255e-16
MC.8	93	131	8.361014	-20.466434	88.932868	3.900838e-14
BQ.1.1.30	19	132	7.751354	-88.464439	224.928877	1.145864e-43
XEK.2	67	118	7.581529	-2.418471	52.836942	2.679179e-06		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9365_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13517_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T,
18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G,
22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T,
25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28600_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

 Case 122 (XFN): OZ271486



Target: 27 samples           Number of changes: 135                                                                          
BC: KP.2.3 + XEC.4.1 + KP.2.3 BC BR: 123-124, 131-132                   BC BR coord: 28271 - 28272, 28883 - 28884      
Direction L1: >>             Initial region span: 1-123,124-126,132-135 Gap history (edge excluded): 123-132 -> 126-132
Alt. candidates: [], []                                                                                                             
Model 1BP/2BP comparison:    2BP vs 1BP: 4.63e-03                                                                                   
Rec. model vs L1: 4.36e-09   Rec. model vs L2: 1.48e-44                                                                      
Flags: Model_2BP_Best

KP.2.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3	4440	123	133.652410	NaN	NaN	NaN	*	*	*
JN.1.16.1	466	116	128.041960	123.352610	61.294779	2.479596e-07
KP.3.3	1715	125	125.747112	114.990543	78.018914	5.774410e-11
KP.3	769	116	125.731619	120.990329	66.019342	2.329563e-08
KP.2	1589	116	120.652034	125.142993	57.714014	1.485142e-06
MC.24.1	25	125	115.041345	104.833621	98.332759	2.245159e-15
XEC.32	42	125	114.306283	103.719070	100.561861	7.362220e-16
JN.1.4	8971	116	112.685369	116.216513	75.566974	1.965705e-10
KP.3.1.1	12013	116	111.034729	115.401754	77.196492	8.700983e-11
XEC.39	155	125	110.386042	99.718248	108.563504	1.348438e-17

|||||

XEC.4.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4.1	68	126	8.142610	NaN	NaN	NaN	*	*	*
KP.3.3.8	15	125	6.591671	-7.964799	39.929598	4.483978e-06		*
XEC.23	142	125	6.591671	-7.964799	39.929598	4.483978e-06		*
XEC.4.3	10	125	6.591671	-13.567013	51.134026	1.658114e-08		*
XEC.24.1	18	125	6.591671	-14.167917	52.335834	9.054536e-09		*
NP.1	16	125	6.591671	-7.964799	39.929598	4.483978e-06		*
XEK.6	23	125	6.591671	-7.964799	39.929598	4.483978e-06		*
XEC.2.3.1	19	125	6.591671	-7.964799	39.929598	4.483978e-06		*
XEP.1	13	125	6.591671	-14.409436	52.818873	7.122550e-09		*
XEK.1	88	125	6.591671	-7.918279	39.836558	4.690366e-06		*

|||||

KP.2.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3	4440	132	4.91084	None	None	None	*	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3695_C|T, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9365_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G,
18492_A|G, 18781_G|A, 18894_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G,
22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T,
25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28462_C|T, 28516_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

 Case 122 (XFN): OZ276300



Target: 27 samples           Number of changes: 134                                                                          
BC: KP.2.3 + XEC.4.1 + KP.2.3 BC BR: 122-123, 130-131                   BC BR coord: 28271 - 28272, 28883 - 28884      
Direction L1: >>             Initial region span: 1-122,123-125,131-134 Gap history (edge excluded): 122-131 -> 125-131
Alt. candidates: [], []                                                                                                             
Model 1BP/2BP comparison:    2BP vs 1BP: 4.63e-03                                                                                   
Rec. model vs L1: 4.39e-09   Rec. model vs L2: 1.65e-44                                                                      
Flags: Model_2BP_Best

KP.2.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3	4440	122	137.290877	NaN	NaN	NaN	*	*	*
KP.3.3	1715	124	129.194732	118.438164	71.123672	4.799137e-11
KP.3	769	115	128.981091	124.239801	59.520397	1.585153e-08
JN.1.16.1	466	115	127.786931	123.097581	61.804837	5.069620e-09
KP.2	1589	115	123.826221	128.317179	51.365642	9.328700e-07
MC.24.1	25	124	118.708832	108.501108	90.997784	2.313534e-15
XEC.32	42	124	118.055414	107.468201	93.063599	8.259479e-16
JN.1.4	8971	115	116.256724	119.787868	68.424264	1.851231e-10
KP.3.1.1	12013	115	114.609095	118.976120	70.047760	8.194277e-11
XEC.39	155	124	113.987950	103.320155	101.359689	1.302059e-17

|||||

XEC.4.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4.1	68	125	8.142610	NaN	NaN	NaN	*	*	*
KP.3.3.4	292	124	6.591671	-7.919257	37.838514	4.690366e-06		*
XEC.24.1	18	124	6.591671	-14.167917	50.335834	9.054536e-09		*
NP.1	16	124	6.591671	-7.964799	37.929598	4.483978e-06		*
XEC.2.3.1	19	124	6.591671	-7.964799	37.929598	4.483978e-06		*
XEK.1	88	124	6.591671	-7.918279	37.836558	4.690366e-06		*
XEC.11.1.1	12	124	6.591671	-7.964799	37.929598	4.483978e-06		*
XEK.2	67	124	6.591671	-7.903241	37.806482	4.761252e-06		*
XEP.1	13	124	6.591671	-14.409436	50.818873	7.122550e-09		*
XEK.6	23	124	6.591671	-7.964799	37.929598	4.483978e-06		*

|||||

KP.2.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3	4440	131	4.91084	None	None	None	*	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3695_C|T, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9365_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10228_C|T, 11042_G|T, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18781_G|A,
18894_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G, 22895_G|C,
22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T,
25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28462_C|T, 28516_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

 Case 122 (XFN): OZ276328



Target: 27 samples           Number of changes: 135                                                                          
BC: KP.2.3 + XEC.4.1 + KP.2.3 BC BR: 123-124, 131-132                   BC BR coord: 28271 - 28272, 28883 - 28884      
Direction L1: >>             Initial region span: 1-123,124-126,132-135 Gap history (edge excluded): 123-132 -> 126-132
Alt. candidates: [], []                                                                                                             
Model 1BP/2BP comparison:    2BP vs 1BP: 4.63e-03                                                                                   
Rec. model vs L1: 4.36e-09   Rec. model vs L2: 1.66e-44                                                                      
Flags: Model_2BP_Best

KP.2.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3	4440	123	133.669686	NaN	NaN	NaN	*	*	*
KP.3.3	1715	125	125.611888	114.855319	78.289361	4.970080e-11
KP.3	769	116	125.434961	120.693671	66.612657	1.708611e-08
JN.1.16.1	466	116	124.192687	119.503337	68.993325	5.197958e-09
KP.2	1589	116	120.275623	124.766581	58.466838	1.000511e-06
MC.24.1	25	125	115.066811	104.859087	98.281825	2.267723e-15
XEC.32	42	125	114.413394	103.826180	100.347639	8.055552e-16
JN.1.4	8971	116	112.653194	116.184339	75.631323	1.879209e-10
KP.3.1.1	12013	116	111.026735	115.393760	77.212480	8.528692e-11
XEC.39	155	125	110.411509	99.743714	108.512571	1.361990e-17

|||||

XEC.4.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4.1	68	126	8.142610	NaN	NaN	NaN	*	*	*
XEC.4.3	10	125	6.591671	-13.567013	53.134026	1.658114e-08		*
XEC.18.3	13	125	6.591671	-13.646512	53.293025	1.530632e-08		*
KP.3.3.8	15	125	6.591671	-7.964799	41.929598	4.483978e-06		*
XEC.23	142	125	6.591671	-7.964799	41.929598	4.483978e-06		*
XEC.24.1	18	125	6.591671	-14.167917	54.335834	9.054536e-09		*
NP.1	16	125	6.591671	-7.964799	41.929598	4.483978e-06		*
XEK.6	23	125	6.591671	-7.964799	41.929598	4.483978e-06		*
XEC.2.3.1	19	125	6.591671	-7.964799	41.929598	4.483978e-06		*
XEP.1	13	125	6.591671	-14.409436	54.818873	7.122550e-09		*

|||||

KP.2.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3	4440	132	4.91084	None	None	None	*	*	*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3695_C|T, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9365_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G,
18781_G|A, 18894_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G,
22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T,
25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28462_C|T, 28516_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

 Case 122 (XFN): OZ284692



Target: 27 samples          Number of changes: 152                                                                    
BC: KP.2.3 + XEC.32 + KP.2.3 BC BR: 140-141, 148-149                   BC BR coord: 28271 - 28272, 28957 - 28958
Direction L1: >>            Initial region span: 1-140,141-148,149-152 Gap history (edge excluded): 140-149 ->  
Alt. candidates: [], []                                                                                                      
Model 1BP/2BP comparison:   2BP vs 1BP: 4.25e-05                                                                             
Rec. model vs L1: 2.34e-14  Rec. model vs L2: 1.43e-12                                                                
Flags: Model_2BP_Best

KP.2.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3	4440	140	156.531125	NaN	NaN	NaN	*	*	*
KP.3	769	150	151.054609	145.961926	38.076148	1.892873e-07
KP.3.1.1	12013	152	147.503128	146.285899	37.428202	2.619794e-07
JN.1.16.1	466	133	143.561260	138.871909	52.256181	1.577515e-10
KP.3.3	1715	150	140.815299	128.413391	73.173219	4.543858e-15
KP.2	1589	133	140.361372	144.852331	40.295339	6.238132e-08
XEC.2	921	150	139.513966	127.153776	75.692448	1.288884e-15
LF.7	58	108	138.501975	130.720924	68.558152	4.554844e-14
XEC.32	42	150	137.785198	110.510255	108.979490	7.609954e-23
JN.1	17255	133	134.267447	138.417538	53.164925	1.005868e-10

|||||

XEC.32 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.32	42	141	18.594804	NaN	NaN	NaN	*	*	*
XBB.2.6	343	142	6.614007	-3.385993	26.771986	2.845819e-10		*
XEC.21	38	145	6.222233	3.592608	12.814784	3.059023e-07
XEC.24.1	18	145	6.222233	-2.610510	25.221020	6.177113e-10
XEC.2.3.1	19	145	6.222233	3.592608	12.814784	3.059023e-07
XEC.2.6	13	145	6.222233	-3.851256	27.702511	1.787559e-10
XEC.22	23	145	6.222233	3.592608	12.814784	3.059023e-07
XEC.23	142	145	6.222233	3.592608	12.814784	3.059023e-07
XEC.24	11	145	6.222233	-2.610510	25.221020	6.177113e-10
XEC.25	13	145	6.222233	3.512565	12.974870	2.823834e-07

|||||

KP.2.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3	4440	149	4.91084	None	None	None	*	*	*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4885_T|C, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8393_G|A, 9344_C|T,
9365_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11681_C|T, 11727_G|A, 12193_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G, 22895_G|C, 22896_T|A,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23580_G|C, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T,
25006_C|T, 25207_C|T, 25584_C|T, 25683_T|C, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28600_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

 Case 122 (XFN): OZ284784



Target: 27 samples             Number of changes: 149                                                          
BC: KP.2.3 + XEC.4.1.4 + KP.2.3 BC BR: 3-4, 7-8                   BC BR coord: 241 - 242, 2789 - 2790    
Direction L1: <<               Initial region span: 1-3,5-7,8-149 Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []                                                                                               
Model 1BP/2BP comparison:      2BP vs 1BP: 4.80e-01                                                                   
Rec. model vs L1: 5.44e-09     Rec. model vs L2: 1.90e-51                                                      
Flags: Model_2BP_Best

KP.2.3 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3	4440	3	3.778452	None	None	None	*	*	*

|||||

XEC.4.1.4 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
XEC.4.1.4	23	5	11.000655	NaN	NaN	NaN	*	*	*
XEC.13	30	5	11.000655	1.000655	5.998691	1.0	*	*
XEC.32	42	5	11.000655	1.000655	5.998691	1.0	*	*
XEC.8.1	12	5	11.000655	1.000655	5.998691	1.0	*	*
XEC.18.3	13	5	11.000655	1.000655	5.998691	1.0	*	*
XEC.18.2	10	5	11.000655	1.000655	5.998691	1.0	*	*
XEC.17	13	5	11.000655	1.000655	5.998691	1.0	*	*
XEC.16	23	5	11.000655	1.000655	5.998691	1.0	*	*
XEC.4.7	13	5	11.000655	1.000655	5.998691	1.0	*	*
XEC.35.1	28	5	11.000655	1.000655	5.998691	1.0	*	*

|||||

KP.2.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3	4440	8	177.246779	NaN	NaN	NaN	*	*	*
KP.3.1.1	12013	5	174.719309	177.550075	-37.100151	3.096183e-02	*
KP.3	769	8	170.987129	175.600349	-33.200698	4.405066e-03	*	*
KP.3.3	1715	5	170.138538	168.366230	-18.732459	3.175644e-06
KP.2	1589	8	168.951364	173.609055	-29.218110	6.021524e-04	*	*
XEC.32	42	5	167.115100	158.104405	1.791191	1.111656e-10
KP.3.1	1957	5	164.156223	165.619134	-13.238267	2.040298e-07
XEC.14	193	6	163.084371	157.250667	3.498666	4.727687e-11
JN.1	17255	8	162.512873	165.522859	-13.045717	1.855391e-07		*
JN.1.16.1	466	8	162.165099	166.493511	-14.987022	4.894419e-07		*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 375_A|G, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9365_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16173_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22594_C|T, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28600_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

 Case 122 (XFN): OZ286973



Target: 27 samples         Number of changes: 149                                                       
BC: JN.1.16.1 + KP.3.3.10  BC BR: 129-130                    BC BR coord: 27263 - 27264          
Direction L1: >>           Initial region span: 1-129,132-149 Gap history (edge excluded): 129-132
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 3.63e-19 Rec. model vs L2: 1.14e-33                                                   
Flags: Model_2BP_Bad_L1_opp

JN.1.16.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.16.1	466	129	172.578324	NaN	NaN	NaN	*	*	*
XEC.32	42	147	167.785198	160.017457	-34.034915	3.492125e-06
MC.24.1	25	129	166.419119	166.419119	-46.838238	2.112253e-03	*	*
XEC.39	155	129	165.916189	165.916189	-45.832379	1.274757e-03	*	*
KP.3	769	129	165.747551	165.747551	-45.495103	1.080858e-03	*	*
KP.3.1.1	12013	149	165.604646	159.220535	-32.441069	1.576978e-06
KP.3.3	1715	129	164.503789	164.503789	-43.007578	3.112233e-04	*	*
XEC.14	193	129	161.700616	161.700616	-37.401232	1.883112e-05	*	*
KP.2	1589	137	160.360936	160.095924	-34.191849	3.782974e-06
XEC.8	592	147	155.612318	146.105693	-6.211385	3.177266e-12

|||||

KP.3.3.10 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.3.10	55	132	21.967750	NaN	NaN	NaN	*	*	*
XEC.2.2	273	132	19.186886	-0.813114	45.626228	6.172909e-02	*	*
XEC.32	42	132	19.087602	-0.912398	45.824796	5.613476e-02	*	*
KP.3.1.1	12013	131	16.384112	6.384112	31.231776	8.268184e+01	*	*
LP.8.1	1124	132	15.415830	-4.584170	53.168340	1.422983e-03	*	*
JN.1.11.1	226	139	12.160138	-8.318174	60.636348	3.397111e-05	*
KR.1.4	24	146	10.910774	-33.066710	110.133420	6.088255e-16
XEC.8	592	131	10.694884	0.694884	42.610233	2.794310e-01	*	*
XEC.2	921	131	10.238426	0.238426	43.523149	1.772844e-01	*	*
XEC.17	13	132	9.123188	-10.876812	65.753625	2.639292e-06		*

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9365_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C,
17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20914_A|C, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23557_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27323_C|T, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28600_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

 Case 122 (XFN): OZ288044



Target: 27 samples         Number of changes: 146                                                       
BC: JN.1.16.1 + KP.3.3.10  BC BR: 127-128                    BC BR coord: 27263 - 27264          
Direction L1: >>           Initial region span: 1-127,135-146 Gap history (edge excluded): 127-135
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 3.61e-19 Rec. model vs L2: 1.77e-40                                                   
Flags: Model_2BP_Bad_L1_opp

JN.1.16.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.16.1	466	127	178.279539	NaN	NaN	NaN	*	*	*
KP.3.3	1715	144	177.577207	169.847037	-53.694074	2.171331e-04	*
XEC.16	23	144	172.335345	164.532019	-43.064037	1.067704e-06
XEC.39	155	144	170.406722	162.642357	-39.284713	1.613000e-07
MC.24.1	25	144	168.792999	162.297526	-38.595051	1.148085e-07
KP.2.3	4440	133	167.817671	158.350575	-30.701150	2.210604e-09
KP.3.1	1957	146	166.569726	157.542921	-29.085842	9.883344e-10
KP.2	1589	127	166.185206	166.185206	-46.370413	5.587380e-06		*
XEC.14	193	144	165.123157	157.646073	-29.292146	1.092278e-09
KP.3.1.1	12013	146	163.310339	157.002670	-28.005340	5.759502e-10

|||||

KP.3.3.10 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.3.10	55	135	23.206758	NaN	NaN	NaN	*	*	*
XEC.2.2	273	135	20.429564	9.186886	23.626228	6.172909e-02	*	*
KP.3.1	1957	129	19.026805	9.026805	23.946390	5.260206e-02	*
KP.3.1.1	12013	129	16.307669	6.307669	29.384662	3.482517e-03	*
KR.1.4	24	143	10.910774	-23.066710	88.133420	6.088255e-16
XEC.32	42	135	10.362196	-5.914595	53.829189	1.708611e-08		*
MR.1	17	135	10.362196	-0.876812	43.753625	2.639292e-06		*
XEC.16	23	135	10.362196	-0.876812	43.753625	2.639292e-06		*
MR.2	14	135	10.362196	-0.876812	43.753625	2.639292e-06		*
XEC.17	13	135	10.362196	-0.876812	43.753625	2.639292e-06		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9365_C|T, 9424_A|G, 9430_C|T, 9534_C|T,
10029_C|T, 10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T,
18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20168_A|C, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 27828_C|T, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

 Case 122 (XFN): OZ288054



Target: 27 samples         Number of changes: 136                                                       
BC: JN.1.16.1 + KP.3.3.10  BC BR: 117-118                    BC BR coord: 27263 - 27264          
Direction L1: >>           Initial region span: 1-117,125-136 Gap history (edge excluded): 117-125
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 3.61e-19 Rec. model vs L2: 9.95e-36                                                   
Flags: Model_2BP_Bad_L1_opp

JN.1.16.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.16.1	466	117	142.396306	NaN	NaN	NaN	*	*	*
KP.3.3	1715	134	129.836921	122.106751	35.786497	1.542286e-09
KP.3.1	1957	136	127.271158	118.244353	43.511294	3.249288e-11
KP.2	1589	117	121.319053	121.319053	37.361894	7.034671e-10		*
KP.3.1.1	12013	136	117.671911	111.364242	57.271515	3.340737e-14
MC.24.1	25	134	117.528579	111.033106	57.933789	2.401735e-14
KP.3	769	117	116.660774	116.660774	46.678452	6.659345e-12		*
XEC.16	23	134	114.909623	107.106296	65.787408	4.717889e-16
KP.2.3	4440	123	110.466941	100.999845	78.000310	1.052883e-18
JN.1	17255	117	110.270646	110.270646	59.458708	1.117609e-14		*

|||||

KP.3.3.10 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.3.10	55	125	23.206758	NaN	NaN	NaN	*	*	*
XEC.2.2	273	125	20.429564	9.186886	23.626228	6.172909e-02	*	*
KP.3.1	1957	119	19.026805	9.026805	23.946390	5.260206e-02	*
KP.3.1.1	12013	119	16.307669	6.307669	29.384662	3.482517e-03	*
KR.1.4	24	133	10.910774	-23.066710	88.133420	6.088255e-16
XEC.32	42	125	10.362196	-5.914595	53.829189	1.708611e-08		*
MR.1	17	125	10.362196	-0.876812	43.753625	2.639292e-06		*
XEC.16	23	125	10.362196	-0.876812	43.753625	2.639292e-06		*
MR.2	14	125	10.362196	-0.876812	43.753625	2.639292e-06		*
XEC.17	13	125	10.362196	-0.876812	43.753625	2.639292e-06		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9365_C|T, 9424_A|G, 9430_C|T, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G,
18894_C|T, 19955_C|T, 20055_A|G, 20168_A|C, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G, 22895_G|C,
22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23629_T|C, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T,
25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 27828_C|T, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

 Case 122 (XFN): OZ288074



Target: 27 samples              Number of changes: 146                                                                
BC: KP.3.1.1 + LF.7.9 + KP.3.1.1 BC BR: 34-35, 49-50                   BC BR coord: 12906 - 12907, 21710 - 21711
Direction L1: <<                Initial region span: 1-34,35-49,50-146 Gap history (edge excluded): 34-50 ->    
Alt. candidates: [], []                                                                                                      
Model 1BP/2BP comparison:       2BP vs 1BP: 9.53e-19                                                                         
Rec. model vs L1: 1.50e-63      Rec. model vs L2: 3.88e-99                                                            
Flags: Model_2BP_Best

KP.3.1.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.1	12013	34	21.881532	None	None	None	*	*	*

|||||

LF.7.9 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
LF.7.9	20	35	17.551727	NaN	NaN	NaN	*	*	*
PY.4	10	37	13.961332	9.541598	38.916805	3.321247e-04	*
PL.1.1	12	48	11.544410	3.156059	51.687881	5.601843e-07
LF.7.1.10	13	48	11.464368	-3.517815	65.035631	7.069932e-10
XFG.2	500	48	11.370057	-6.264129	70.528257	4.542311e-11
LF.7.3.5	16	48	11.256728	-4.542545	67.085090	2.536667e-10
XFJ.1	59	48	11.204542	-4.292347	66.584694	3.273471e-10
PY.2	17	48	11.196104	-4.432754	66.865509	2.831626e-10
XFG.3.1	87	48	11.161286	0.649296	56.701408	4.575339e-08
XFG.3	480	48	10.946573	-4.000604	66.001207	4.374757e-10

|||||

KP.3.1.1 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.1.1	12013	50	143.744428	NaN	NaN	NaN	*	*	*
PG.3	31	50	140.430068	155.840527	-33.681053	5.628964e-05	*	*
KP.2.3	4440	50	139.220879	149.072326	-20.144653	6.460332e-08		*
XEC.32	42	60	136.702794	140.012977	-2.025953	7.546026e-12
KP.3.3.2	217	50	136.312808	126.824332	24.351335	1.410503e-17		*
KP.3.1	1957	48	135.311718	140.362613	-2.725225	1.070832e-11
JN.1	17255	9	132.336765	134.689354	8.621291	3.673671e-14
PG.6	23	50	131.523507	133.621942	10.756115	1.260100e-14		*
KP.3	769	48	126.270755	121.750348	34.499304	8.817178e-20
XEC.2.2	273	60	124.191888	136.003953	5.992094	1.368351e-13

Target sequence

, 21_C|T, 44_C|T, 241_C|T, 515_520, 670_T|G, 897_C|A, 2060_G|A, 2585_2587, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5104_T|C, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9365_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 17934_C|A, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20914_A|C, 21641_G|T, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T,
22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A,
22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25592_A|G, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28600_T|C,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

 Case 122 (XFN): OZ288105



Target: 27 samples         Number of changes: 136                                                       
BC: JN.1.16.1 + KP.3.3.10  BC BR: 118-119                    BC BR coord: 27263 - 27264          
Direction L1: >>           Initial region span: 1-118,126-136 Gap history (edge excluded): 118-126
Alt. candidates: [], []                                                                                        
Model 1BP/2BP comparison:  -                                                                                   
Rec. model vs L1: 4.61e-19 Rec. model vs L2: 7.38e-42                                                   
Flags: Model_2BP_Bad_L1_opp

JN.1.16.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.16.1	466	118	142.849571	NaN	NaN	NaN	*	*	*
KP.3.3	1715	134	118.318237	112.080283	51.839433	4.332702e-14
KP.3.1.1	12013	136	116.449369	111.651598	52.696805	2.818462e-14
KP.3.1	1957	136	115.902597	108.292437	59.415126	9.790000e-16
KP.2.3	4440	124	111.447986	101.980890	72.038220	1.779855e-18
KP.2	1589	118	111.386318	111.386318	53.227365	2.162341e-14		*
JN.1	17255	118	109.687913	109.687913	56.624174	3.970041e-15		*
KP.3	769	118	106.659750	106.659750	62.680499	1.918151e-16		*
MC.24.1	25	134	106.139391	101.201324	73.597352	8.158960e-19
JN.1.4	8971	118	105.217185	105.217185	65.565631	4.521965e-17		*

|||||

KP.3.3.10 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.3.3.10	55	126	21.649352	NaN	NaN	NaN	*	*	*
XEC.2.2	273	126	18.939203	7.696525	26.606951	6.620495e-02	*	*
KP.3.1	1957	120	17.610160	7.610160	26.779680	6.081006e-02	*
KP.3.1.1	12013	120	14.797771	4.797771	32.404458	3.661069e-03	*
KR.1.4	24	133	10.910774	-24.624117	91.248234	6.088255e-16
XEK.2	67	126	8.820538	-2.418471	46.836942	2.679179e-06		*
MR.1	17	126	8.804789	-2.434219	46.868439	2.639292e-06		*
XEC.4.7	13	126	8.804789	-2.434219	46.868439	2.639292e-06		*
XEC.32	42	126	8.804789	-7.472002	56.944003	1.717175e-08		*
XEC.17	13	126	8.804789	-2.434219	46.868439	2.639292e-06		*

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9365_C|T, 9424_A|G, 9430_C|T, 9534_C|T,
10029_C|T, 10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T,
18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20168_A|C, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T,
22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23629_T|C, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T,
24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 27828_C|T, 28271_A|T, 28291_C|A, 28311_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

 Case 122 (XFN): OZ288128



Target: 27 samples        Number of changes: 139                                                   
BC: JN.1.16.1 + KP.2.3    BC BR: 44-45                    BC BR coord: 21653 - 21654        
Direction L1: <<          Initial region span: 1-43,45-139 Gap history (edge excluded): 43-45
Alt. candidates: [], []                                                                                   
Model 1BP/2BP comparison: 1BP vs 2BP: 9.81e-07                                                            
Rec. model vs L1: 1.14e-42 Rec. model vs L2: 1.43e-25                                               
Flags: Model_1BP_Best

JN.1.16.1 >>

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
JN.1.16.1	466	43	46.216326	NaN	NaN	NaN	*	*	*
JN.1	17255	43	36.251832	17.494911	85.010178	1.259671e-10		*
XEC.25	13	36	30.934459	-7.590022	135.180043	1.606868e-21
JN.1.7	1974	43	28.153578	10.423381	99.153238	1.071014e-13		*
XEC.17	13	36	27.463722	-11.541015	143.082029	3.093976e-23
KP.3.1.1	12013	32	27.333999	-7.587713	135.175426	1.606868e-21
KP.3.3	1715	36	27.043808	4.468359	111.063282	2.776973e-16
XEC.39	155	36	25.899451	-12.579296	145.158593	1.093580e-23
XEC.16	23	15	24.119754	-24.312403	168.624807	8.801901e-29
XEC.18.3	13	15	24.119754	-32.642224	185.284448	2.122772e-32

|||||

KP.2.3 <<

	num_seq	t_ch_MAX	max_CL	CL@BC_t_ch_MAX	aic	PV	PV_OK	t_ch_MAX_OK	phyl_OK
KP.2.3	4440	45	131.390260	NaN	NaN	NaN	*	*	*
KP.3.1.1	12013	45	124.322999	124.322999	-40.645999	8.544949e-04	*	*
PG.3	31	45	114.960379	114.960379	-21.920757	7.320515e-08		*
KP.3	769	25	107.691914	93.532616	20.934768	3.628962e-17
KP.3.1	1957	25	106.719037	103.805175	0.389649	1.047097e-12
KP.3.3	1715	1	102.447114	97.978754	12.042491	3.091871e-15
XEC.2.2	273	54	98.911785	91.998845	24.002310	7.818805e-18
KP.2	1589	25	97.364066	93.601235	20.797529	3.872679e-17
KP.3.3.10	55	25	97.331456	94.210473	19.579053	7.127400e-17
KP.3.3.2	217	54	96.121273	94.976707	18.046586	1.531674e-16

Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5577_T|C, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9322_T|C, 9344_C|T, 9365_C|T, 9424_A|G,
9430_C|T, 9534_C|T, 10029_C|T, 10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T,
22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T,
22865_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23856_G|T, 23948_G|T, 24058_C|T, 24378_C|T, 24424_A|T,
24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27059_C|T, 27259_A|C,
27321_A|G, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28031_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T,
29734_29759

Target: 9 samples	Number of changes: 146
BC: LF.7.9 + A.2.5.1 + LF.7.9	BC BR: 134-135, 136-137	BC BR coord: 27810 - 27811, 28145 - 28146
Direction L1: >>	Initial region span: 1-134,135-136,141-146	Gap history (edge excluded): 134-141 -> 136-141
Alt. candidates: [], []
Model 1BP/2BP comparison:	2BP vs 1BP: 5.93e-02
Rec. model vs L1: 2.89e-16	Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

Target: 9 samples	Number of changes: 151
BC: XFJ.1 + MC.2	BC BR: 119-120	BC BR coord: 25216 - 25217
Direction L1: >>	Initial region span: 1-119,123-151	Gap history (edge excluded): 119-123
Alt. candidates: [], []
Model 1BP/2BP comparison:	1BP vs 2BP: 1.89e-02
Rec. model vs L1: 1.18e-60	Rec. model vs L2: 3.06e-139
Flags: Model_1BP_Best

Target: 9 samples	Number of changes: 149
BC: KP.2.28.1 + XFJ.1	BC BR: 12-13	BC BR coord: 5240 - 5241
Direction L1: <<	Initial region span: 1-8,13-149	Gap history (edge excluded): 8-13
Alt. candidates: [], []
Model 1BP/2BP comparison:	1BP vs 2BP: 4.71e-02
Rec. model vs L1: 1.61e-129	Rec. model vs L2: 2.57e-25
Flags: Model_1BP_Best

Target: 9 samples	Number of changes: 154
BC: MC.11 + XFJ.1	BC BR: 17-18	BC BR coord: 5240 - 5241
Direction L1: <<	Initial region span: 1-11,18-154	Gap history (edge excluded): 11-18
Alt. candidates: [], []
Model 1BP/2BP comparison:	1BP vs 2BP: 2.45e-02
Rec. model vs L1: 3.93e-154	Rec. model vs L2: 2.20e-30
Flags: Model_1BP_Best

Target: 9 samples	Number of changes: 152
BC: MC.17.1 + XFJ.1	BC BR: 17-18	BC BR coord: 5240 - 5241
Direction L1: <<	Initial region span: 1-6,18-152	Gap history (edge excluded): 6-18
Alt. candidates: [], []
Model 1BP/2BP comparison:	-
Rec. model vs L1: 3.65e-182	Rec. model vs L2: 5.83e-26
Flags: Model_2BP_Bad_L1_opp

Target: 9 samples	Number of changes: 151
BC: XFJ.1 + MC.13	BC BR: 120-121	BC BR coord: 25216 - 25217
Direction L1: >>	Initial region span: 1-120,124-151	Gap history (edge excluded): 120-124
Alt. candidates: [], []
Model 1BP/2BP comparison:	-
Rec. model vs L1: 5.32e-45	Rec. model vs L2: 8.98e-170
Flags: Model_2BP_Bad_L1_opp

Target: 9 samples	Number of changes: 150
BC: XFJ.3 + MC.13	BC BR: 119-120	BC BR coord: 25216 - 25217
Direction L1: >>	Initial region span: 1-119,123-150	Gap history (edge excluded): 119-123
Alt. candidates: [], []
Model 1BP/2BP comparison:	-
Rec. model vs L1: 2.02e-47	Rec. model vs L2: 2.13e-163
Flags: Model_2BP_Bad_L1_opp

Target: 9 samples	Number of changes: 150
BC: XFJ.3 + KP.3.1	BC BR: 119-120	BC BR coord: 25216 - 25217
Direction L1: >>	Initial region span: 1-119,123-150	Gap history (edge excluded): 119-123
Alt. candidates: [], []
Model 1BP/2BP comparison:	1BP vs 2BP: 7.95e-09
Rec. model vs L1: 3.48e-47	Rec. model vs L2: 5.92e-98
Flags: Model_1BP_Best

Target: 9 samples	Number of changes: 153
BC: JN.1.48 + XFJ.1	BC BR: 14-15	BC BR coord: 5240 - 5241
Direction L1: <<	Initial region span: 1-8,18-153	Gap history (edge excluded): 8-18
Alt. candidates: [], []
Model 1BP/2BP comparison:	1BP vs 2BP: 4.71e-02
Rec. model vs L1: 2.36e-104	Rec. model vs L2: 2.57e-25
Flags: Model_1BP_Best

Target: 220 samples	Number of changes: 139
BC: XDY.6 + CK.2	BC BR: 134-135	BC BR coord: 28958 - 28959
Direction L1: >>	Initial region span: 1-134,135-139	Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison:	-
Rec. model vs L1: 6.18e-22	Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Bad_L1_opp

Target: 24 samples	Number of changes: 146
BC: JN.1.53 + XFJ.1	BC BR: 11-12	BC BR coord: 4839 - 4840
Direction L1: <<	Initial region span: 1-9,12-146	Gap history (edge excluded): 9-12
Alt. candidates: [], []
Model 1BP/2BP comparison:	1BP vs 2BP: 5.13e-02
Rec. model vs L1: 1.29e-158	Rec. model vs L2: 3.31e-16
Flags: Model_1BP_Best

Target: 24 samples	Number of changes: 147
BC: LP.8.1 + XFJ.1	BC BR: 12-13	BC BR coord: 4839 - 4840
Direction L1: <<	Initial region span: 1-6,13-147	Gap history (edge excluded): 6-13
Alt. candidates: [], []
Model 1BP/2BP comparison:	1BP vs 2BP: 9.83e-02
Rec. model vs L1: 2.11e-186	Rec. model vs L2: 2.67e-06
Flags: Model_1BP_Best

Target: 24 samples	Number of changes: 144
BC: JN.1.8.1 + XFJ.1	BC BR: 11-12	BC BR coord: 4839 - 4840
Direction L1: <<	Initial region span: 1-11,12-144	Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison:	1BP vs 2BP: 7.19e-05
Rec. model vs L1: 4.87e-121	Rec. model vs L2: 3.58e-21
Flags: Model_1BP_Best

Target: 24 samples	Number of changes: 149
BC: JN.1 + XFJ.1	BC BR: 29-30	BC BR coord: 12771 - 12772
Direction L1: <<	Initial region span: 1-29,30-149	Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison:	1BP vs 2BP: 3.97e-15
Rec. model vs L1: 5.60e-82	Rec. model vs L2: 5.00e-29
Flags: Model_1BP_Best

Target: 24 samples	Number of changes: 148
BC: XFJ.1 + LF.7 + XFJ.1	BC BR: 9-10, 13-14	BC BR coord: 4330 - 4331, 7841 - 7842
Direction L1: <<	Initial region span: 1-9,11-13,14-148	Gap history (edge excluded): 9-14 -> 9-11
Alt. candidates: [], []
Model 1BP/2BP comparison:	2BP vs 1BP: 5.37e-04
Rec. model vs L1: 7.78e-16	Rec. model vs L2: 1.36e-87
Flags: Model_2BP_Best

Target: 24 samples	Number of changes: 146
BC: XFJ.1 + KP.2.5 + XFJ.1	BC BR: 5-6, 11-12	BC BR coord: 3037 - 3038, 5238 - 5239
Direction L1: <<	Initial region span: 1-5,7-11,12-146	Gap history (edge excluded): 5-12 -> 5-7
Alt. candidates: [], []
Model 1BP/2BP comparison:	2BP vs 1BP: 2.32e-05
Rec. model vs L1: 8.95e-16	Rec. model vs L2: 1.60e-202
Flags: Model_2BP_Best

Target: 24 samples	Number of changes: 146
BC: XFJ.1 + GA.4.1 + XFJ.1	BC BR: 138-139, 140-141	BC BR coord: 28361 - 28362, 28877 - 28878
Direction L1: >>	Initial region span: 1-138,139-140,141-146	Gap history (edge excluded): 138-141 ->
Alt. candidates: [], []
Model 1BP/2BP comparison:	2BP vs 1BP: 2.30e-01
Rec. model vs L1: 1.15e-17	Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

Target: 59 samples	Number of changes: 152
BC: KP.3.3 + KP.2.3.15 + KP.3.3	BC BR: 11-12, 16-17	BC BR coord: 4330 - 4331, 6470 - 6471
Direction L1: <<	Initial region span: 1-11,12-16,17-152	Gap history (edge excluded): 11-17 ->
Alt. candidates: [], []
Model 1BP/2BP comparison:	2BP vs 1BP: 1.08e-10
Rec. model vs L1: 9.36e-20	Rec. model vs L2: 4.00e-70
Flags: Model_2BP_Best

Target: 269 samples	Number of changes: 142
BC: KP.2 + KP.3.1.1 + KP.2	BC BR: 10-11, 20-21	BC BR coord: 6183 - 6184, 9533 - 9534
Direction L1: <<	Initial region span: 1-10,13-20,21-142	Gap history (edge excluded): 10-21 -> 10-13
Alt. candidates: [], []
Model 1BP/2BP comparison:	2BP vs 1BP: 1.83e-04
Rec. model vs L1: 7.15e-28	Rec. model vs L2: 9.68e-29
Flags: Model_2BP_Best

Target: 269 samples	Number of changes: 135
BC: KP.2 + LF.7.1.4 + KP.2	BC BR: 8-9, 10-11	BC BR coord: 6183 - 6184, 7118 - 7119
Direction L1: <<	Initial region span: 1-8,9-10,12-135	Gap history (edge excluded): 8-12 -> 10-12
Alt. candidates: [], []
Model 1BP/2BP comparison:	2BP vs 1BP: 1.34e-08
Rec. model vs L1: 2.65e-19	Rec. model vs L2: 6.49e-120
Flags: Model_2BP_Best

Target: 269 samples	Number of changes: 146
BC: JN.1 + KP.2	BC BR: 20-21	BC BR coord: 8866 - 8867
Direction L1: <<	Initial region span: 1-19,21-146	Gap history (edge excluded): 19-21
Alt. candidates: [], []
Model 1BP/2BP comparison:	1BP vs 2BP: 2.08e-15
Rec. model vs L1: 1.10e-21	Rec. model vs L2: 3.08e-35
Flags: Model_1BP_Best

Target: 269 samples	Number of changes: 138
BC: KS.1.1.2 + MC.24.1	BC BR: 40-41	BC BR coord: 17411 - 17412
Direction L1: <<	Initial region span: 1-34,43-138	Gap history (edge excluded): 34-43
Alt. candidates: [], []
Model 1BP/2BP comparison:	1BP vs 2BP: 2.49e-16
Rec. model vs L1: 4.77e-36	Rec. model vs L2: 1.53e-36
Flags: Model_1BP_Best

Target: 269 samples	Number of changes: 145
BC: LB.1.3.2 + KP.2	BC BR: 13-14	BC BR coord: 7118 - 7119
Direction L1: <<	Initial region span: 1-10,16-145	Gap history (edge excluded): 10-16
Alt. candidates: [], []
Model 1BP/2BP comparison:	1BP vs 2BP: 9.01e-07
Rec. model vs L1: 4.68e-67	Rec. model vs L2: 1.32e-16
Flags: Model_1BP_Best

Target: 269 samples	Number of changes: 147
BC: MC.24.1 + LB.1.7 + MC.24.1	BC BR: 3-4, 43-44	BC BR coord: 896 - 897, 17409 - 17410
Direction L1: <<	Initial region span: 1-3,17-43,44-147	Gap history (edge excluded): 3-44 -> 3-17
Alt. candidates: [], []
Model 1BP/2BP comparison:	2BP vs 1BP: 3.13e-28
Rec. model vs L1: 5.52e-38	Rec. model vs L2: 2.52e-54
Flags: Model_2BP_Best

Target: 269 samples	Number of changes: 145
BC: XEC.2 + KP.3	BC BR: 136-137	BC BR coord: 28271 - 28272
Direction L1: >>	Initial region span: 1-136,137-145	Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison:	1BP vs 2BP: 5.73e-02
Rec. model vs L1: 8.12e-19	Rec. model vs L2: 1.35e-28
Flags: Model_1BP_Best

Target: 269 samples	Number of changes: 146
BC: KP.2 + CK.1	BC BR: 142-143	BC BR coord: 28958 - 28959
Direction L1: >>	Initial region span: 1-142,143-146	Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison:	-
Rec. model vs L1: 7.43e-14	Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Bad_L1_opp

Target: 269 samples	Number of changes: 143
BC: JN.1 + MC.24.1	BC BR: 40-41	BC BR coord: 16949 - 16950
Direction L1: <<	Initial region span: 1-28,41-143	Gap history (edge excluded): 28-41
Alt. candidates: [], []
Model 1BP/2BP comparison:	1BP vs 2BP: 9.38e-11
Rec. model vs L1: 5.29e-29	Rec. model vs L2: 4.13e-44
Flags: Model_1BP_Best

Target: 269 samples	Number of changes: 139
BC: JN.9 + KP.2	BC BR: 11-12	BC BR coord: 7118 - 7119
Direction L1: <<	Initial region span: 1-11,12-139	Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison:	1BP vs 2BP: 4.90e-02
Rec. model vs L1: 5.28e-125	Rec. model vs L2: 2.54e-32
Flags: Model_1BP_Best

Target: 269 samples	Number of changes: 144
BC: KP.2 + JN.1.52	BC BR: 136-137	BC BR coord: 28361 - 28362
Direction L1: >>	Initial region span: 1-136,138-144	Gap history (edge excluded): 136-138
Alt. candidates: [], []
Model 1BP/2BP comparison:	-
Rec. model vs L1: 4.01e-07	Rec. model vs L2: 5.24e-64
Flags: Model_2BP_Bad_L1_opp

Target: 530 samples	Number of changes: 152
BC: XFG.3 + FY.1.4.1 + XFG.3	BC BR: 131-132, 136-137	BC BR coord: 26872 - 26873, 27387 - 27388
Direction L1: >>	Initial region span: 1-131,132-136,138-152	Gap history (edge excluded): 131-138 -> 136-138
Alt. candidates: [], []
Model 1BP/2BP comparison:	2BP vs 1BP: 2.97e-01
Rec. model vs L1: 2.86e-08	Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best